Published Histories | delhomme | asp5 cufflinks example
Import history

Galaxy History ' asp5 cufflinks example'


DatasetAnnotation
1: Asp5 Xylem (BAM)
112.9 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
None
2: Asp5 Leaf (BAM)
108.2 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
None
3: Ptrichocarpa_156.gtf
~520,000 lines
format: gtf, database: ?
Info: uploaded gff3 file
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
##gff-version 3K:boooo";
scaffold_1phytozome8_0exon1263212650.+.gene_id "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1phytozome8_05UTR1263212638.+.gene_id "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1phytozome8_0CDS1263912650.+0gene_id "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1phytozome8_0exon1276812891.+.gene_id "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1phytozome8_0CDS1276812891.+0gene_id "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
13: Cufflinks on data 1 and data 3: gene expression
40,669 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 5000 -F 0.050000 -j 0.050000 -p 4 -G /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa
12345678910111213
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
POPTR_0001s00220--POPTR_0001s00220--scaffold_1:74075-75893--000OK
POPTR_0001s00230--POPTR_0001s00230--scaffold_1:80190-81289--000OK
POPTR_0001s00240--POPTR_0001s00240--scaffold_1:105027-107984--000OK
POPTR_0001s00200--POPTR_0001s00200--scaffold_1:12631-13612--000OK
POPTR_0001s00270--POPTR_0001s00270--scaffold_1:137067-139439--000OK
14: Cufflinks on data 1 and data 3: transcript expression
45,013 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 5000 -F 0.050000 -j 0.050000 -p 4 -G /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa
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tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
POPTR_0001s00220.1--POPTR_0001s00220--scaffold_1:74075-7589310710000OK
POPTR_0001s00230.1--POPTR_0001s00230--scaffold_1:80190-812893240000OK
POPTR_0001s00240.1--POPTR_0001s00240--scaffold_1:105027-10798411250000OK
POPTR_0001s00200.1--POPTR_0001s00200--scaffold_1:12631-136125560000OK
POPTR_0001s00270.1--POPTR_0001s00270--scaffold_1:137067-13943912270000OK
15: Cufflinks on data 1 and data 3: assembled transcripts
~280,000 lines
format: gtf, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 5000 -F 0.050000 -j 0.050000 -p 4 -G /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
scaffold_1Cufflinkstranscript74076758931+.gene_id "POPTR_0001s00220"; transcript_id "POPTR_0001s00220.1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon74076742351+.gene_id "POPTR_0001s00220"; transcript_id "POPTR_0001s00220.1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon74359746341+.gene_id "POPTR_0001s00220"; transcript_id "POPTR_0001s00220.1"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon75259758931+.gene_id "POPTR_0001s00220"; transcript_id "POPTR_0001s00220.1"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinkstranscript80191812891-.gene_id "POPTR_0001s00230"; transcript_id "POPTR_0001s00230.1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon80191803851-.gene_id "POPTR_0001s00230"; transcript_id "POPTR_0001s00230.1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
19: Cufflinks on data 2 and data 3: gene expression
40,669 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 5000 -F 0.050000 -j 0.050000 -p 4 -G /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa
12345678910111213
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
POPTR_0001s00230--POPTR_0001s00230--scaffold_1:80190-81289--000OK
POPTR_0001s00240--POPTR_0001s00240--scaffold_1:105027-107984--000OK
POPTR_0001s00200--POPTR_0001s00200--scaffold_1:12631-13612--000OK
POPTR_0001s00210--POPTR_0001s00210--scaffold_1:19768-22804--3.7292308.03538OK
POPTR_0001s00220--POPTR_0001s00220--scaffold_1:74075-75893--1.1003103.30092OK
20: Cufflinks on data 2 and data 3: transcript expression
45,013 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 5000 -F 0.050000 -j 0.050000 -p 4 -G /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa
12345678910111213
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
POPTR_0001s00230.1--POPTR_0001s00230--scaffold_1:80190-812893240000OK
POPTR_0001s00240.1--POPTR_0001s00240--scaffold_1:105027-10798411250000OK
POPTR_0001s00200.1--POPTR_0001s00200--scaffold_1:12631-136125560000OK
POPTR_0001s00210.1--POPTR_0001s00210--scaffold_1:19768-228049830.2637023.7292308.03538OK
POPTR_0001s00220.1--POPTR_0001s00220--scaffold_1:74075-7589310710.07780481.1003103.30092OK
21: Cufflinks on data 2 and data 3: assembled transcripts
~280,000 lines
format: gtf, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 5000 -F 0.050000 -j 0.050000 -p 4 -G /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
scaffold_1Cufflinkstranscript80191812891-.gene_id "POPTR_0001s00230"; transcript_id "POPTR_0001s00230.1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon80191803851-.gene_id "POPTR_0001s00230"; transcript_id "POPTR_0001s00230.1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon81161812891-.gene_id "POPTR_0001s00230"; transcript_id "POPTR_0001s00230.1"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinkstranscript1050281079841+.gene_id "POPTR_0001s00240"; transcript_id "POPTR_0001s00240.1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon1050281053281+.gene_id "POPTR_0001s00240"; transcript_id "POPTR_0001s00240.1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
scaffold_1Cufflinksexon1054861056411+.gene_id "POPTR_0001s00240"; transcript_id "POPTR_0001s00240.1"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
22: Cuffcompare on data 15, data 3, and data 21: transcript accuracy
30 lines
format: txt, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
# Cuffcompare v1.3.0 | Command line was:
#cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
#
#= Summary for dataset: ./input1 :
# Query mRNAs : 45004 in 40622 loci (37514 multi-exon transcripts)
23: Cuffcompare on data 15, data 3, and data 21: 15 data tmap file
45,005 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
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ref_gene_idref_idclass_codecuff_gene_idcuff_idFMIFPKMFPKM_conf_loFPKM_conf_hicovlenmajor_iso_idref_match_len
POPTR_0001s00220POPTR_0001s00220.1=POPTR_0001s00220POPTR_0001s00220.100.0000000.0000000.0000000.0000001071POPTR_0001s00220.11071
POPTR_0001s00230POPTR_0001s00230.1=POPTR_0001s00230POPTR_0001s00230.100.0000000.0000000.0000000.000000324POPTR_0001s00230.1324
POPTR_0001s00240POPTR_0001s00240.1=POPTR_0001s00240POPTR_0001s00240.100.0000000.0000000.0000000.0000001125POPTR_0001s00240.11125
POPTR_0001s00200POPTR_0001s00200.1=POPTR_0001s00200POPTR_0001s00200.100.0000000.0000000.0000000.000000556POPTR_0001s00200.1556
POPTR_0001s00270POPTR_0001s00270.1=POPTR_0001s00270POPTR_0001s00270.100.0000000.0000000.0000000.0000001227POPTR_0001s00270.11227
24: Cuffcompare on data 15, data 3, and data 21: data 15 refmap file
45,005 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
1234
ref_gene_idref_idclass_codecuff_id_list
POPTR_0001s00200POPTR_0001s00200.1=POPTR_0001s00200|POPTR_0001s00200.1
POPTR_0001s00210POPTR_0001s00210.1=POPTR_0001s00210|POPTR_0001s00210.1
POPTR_0001s00220POPTR_0001s00220.1=POPTR_0001s00220|POPTR_0001s00220.1
POPTR_0001s00240POPTR_0001s00240.1=POPTR_0001s00240|POPTR_0001s00240.1
POPTR_0001s00285POPTR_0001s00285.1=POPTR_0001s00285|POPTR_0001s00285.1
25: Cuffcompare on data 15, data 3, and data 21: data 21 tmap file
45,005 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
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ref_gene_idref_idclass_codecuff_gene_idcuff_idFMIFPKMFPKM_conf_loFPKM_conf_hicovlenmajor_iso_idref_match_len
POPTR_0001s00230POPTR_0001s00230.1=POPTR_0001s00230POPTR_0001s00230.100.0000000.0000000.0000000.000000324POPTR_0001s00230.1324
POPTR_0001s00240POPTR_0001s00240.1=POPTR_0001s00240POPTR_0001s00240.100.0000000.0000000.0000000.0000001125POPTR_0001s00240.11125
POPTR_0001s00200POPTR_0001s00200.1=POPTR_0001s00200POPTR_0001s00200.100.0000000.0000000.0000000.000000556POPTR_0001s00200.1556
POPTR_0001s00210POPTR_0001s00210.1=POPTR_0001s00210POPTR_0001s00210.11003.7292340.0000008.0353810.263702983POPTR_0001s00210.1983
POPTR_0001s00220POPTR_0001s00220.1=POPTR_0001s00220POPTR_0001s00220.11001.1003050.0000003.3009150.0778051071POPTR_0001s00220.11071
26: Cuffcompare on data 15, data 3, and data 21: data 21 refmap file
1 line
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
1234
ref_gene_idref_idclass_codecuff_id_list
27: Cuffcompare on data 15, data 3, and data 21: transcript tracking
45,004 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
123456
TCONS_00000001XLOC_000001POPTR_0001s00200|POPTR_0001s00200.1=q1:POPTR_0001s00200|POPTR_0001s00200.1|0|0.000000|0.000000|0.000000|0.000000|556q2:POPTR_0001s00200|POPTR_0001s00200.1|0|0.000000|0.000000|0.000000|0.000000|556
TCONS_00000002XLOC_000002POPTR_0001s00210|POPTR_0001s00210.1=q1:POPTR_0001s00210|POPTR_0001s00210.1|100|2.984940|0.000000|6.431652|0.218858|983q2:POPTR_0001s00210|POPTR_0001s00210.1|100|3.729234|0.000000|8.035381|0.263702|983
TCONS_00000003XLOC_000003POPTR_0001s00220|POPTR_0001s00220.1=q1:POPTR_0001s00220|POPTR_0001s00220.1|0|0.000000|0.000000|0.000000|0.000000|1071q2:POPTR_0001s00220|POPTR_0001s00220.1|100|1.100305|0.000000|3.300915|0.077805|1071
TCONS_00000004XLOC_000004POPTR_0001s00240|POPTR_0001s00240.1=q1:POPTR_0001s00240|POPTR_0001s00240.1|0|0.000000|0.000000|0.000000|0.000000|1125q2:POPTR_0001s00240|POPTR_0001s00240.1|0|0.000000|0.000000|0.000000|0.000000|1125
TCONS_00000005XLOC_000005POPTR_0001s00285|POPTR_0001s00285.1=q1:POPTR_0001s00285|POPTR_0001s00285.1|0|0.000000|0.000000|0.000000|0.000000|891q2:POPTR_0001s00285|POPTR_0001s00285.1|0|0.000000|0.000000|0.000000|0.000000|891
TCONS_00000006XLOC_000006POPTR_0001s00300|POPTR_0001s00300.1=q1:POPTR_0001s00300|POPTR_0001s00300.1|100|8.072222|3.411723|12.732722|0.591861|1451q2:POPTR_0001s00300|POPTR_0001s00300.1|100|9.187962|3.376985|14.998940|0.649699|1451
28: Cuffcompare on data 15, data 3, and data 21: combined transcripts
~230,000 lines
format: gtf, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/002/dataset_2480.dat -s /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa ./input1 ./input2
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
scaffold_1Cufflinksexon1263212650.+.gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "POPTR_0001s00200"; oId "POPTR_0001s00200.1"; nearest_ref "POPTR_0001s00200.1"; class_code "="; tss_id "TSS1"; p_id "P1";
scaffold_1Cufflinksexon1276812891.+.gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "POPTR_0001s00200"; oId "POPTR_0001s00200.1"; nearest_ref "POPTR_0001s00200.1"; class_code "="; tss_id "TSS1"; p_id "P1";
scaffold_1Cufflinksexon1311713226.+.gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "POPTR_0001s00200"; oId "POPTR_0001s00200.1"; nearest_ref "POPTR_0001s00200.1"; class_code "="; tss_id "TSS1"; p_id "P1";
scaffold_1Cufflinksexon1331013612.+.gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "POPTR_0001s00200"; oId "POPTR_0001s00200.1"; nearest_ref "POPTR_0001s00200.1"; class_code "="; tss_id "TSS1"; p_id "P1";
scaffold_1Cufflinksexon1976920136.+.gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "POPTR_0001s00210"; oId "POPTR_0001s00210.1"; nearest_ref "POPTR_0001s00210.1"; class_code "="; tss_id "TSS2"; p_id "P2";
scaffold_1Cufflinksexon2219022804.+.gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "POPTR_0001s00210"; oId "POPTR_0001s00210.1"; nearest_ref "POPTR_0001s00210.1"; class_code "="; tss_id "TSS2"; p_id "P2";
29: Cuffdiff on data 1, data 2, and data 28: isoform expression
45,002 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
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test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
TCONS_00000001XLOC_000001POPTR_0001s00200scaffold_1:12631-13612q1q2NOTEST000011no
TCONS_00000002XLOC_000002POPTR_0001s00210scaffold_1:19768-22804q1q2NOTEST3.73984.429040.244033-0.2071660.835881no
TCONS_00000003XLOC_000003POPTR_0001s00220scaffold_1:74075-75893q1q2NOTEST01.312421.79769e+3081.79769e+3080.1586551no
TCONS_00000004XLOC_000004POPTR_0001s00240scaffold_1:105027-107984q1q2NOTEST000011no
TCONS_00000005XLOC_000005POPTR_0001s00285scaffold_1:154169-155938q1q2NOTEST000011no
30: Cuffdiff on data 1, data 2, and data 28: gene expression
40,623 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
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test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
XLOC_000001XLOC_000001POPTR_0001s00200scaffold_1:12631-13612q1q2NOTEST000011no
XLOC_000002XLOC_000002POPTR_0001s00210scaffold_1:19768-22804q1q2NOTEST3.73984.429040.244033-0.2071660.835881no
XLOC_000003XLOC_000003POPTR_0001s00220scaffold_1:74075-75893q1q2NOTEST01.312421.79769e+3081.79769e+3080.1586551no
XLOC_000004XLOC_000004POPTR_0001s00240scaffold_1:105027-107984q1q2NOTEST000011no
XLOC_000005XLOC_000005POPTR_0001s00285scaffold_1:154169-155938q1q2NOTEST000011no
31: Cuffdiff on data 1, data 2, and data 28: TSS groups expression
41,277 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
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test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
TSS1XLOC_000001POPTR_0001s00200scaffold_1:12631-13612q1q2NOTEST000011no
TSS10XLOC_000009POPTR_0001s00360scaffold_1:249046-255958q1q2NOTEST11.33640-1.79769e+308-1.79769e+3080.06081051no
TSS100XLOC_000096POPTR_0001s02380scaffold_1:1795537-1797212q1q2NOTEST14.25828.65091.00681-0.9530630.3405581no
TSS1000XLOC_000983POPTR_0001s21340scaffold_1:19753744-19759192q1q2NOTEST4.6214731.48292.76815-2.58690.009684311no
TSS10000XLOC_009844POPTR_0012s05100scaffold_12:4588373-4589583q1q2NOTEST01.556831.79769e+3081.79769e+3080.1586551no
32: Cuffdiff on data 1, data 2, and data 28: CDS Expression FPKM Tracking
43,828 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314
test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
P1XLOC_000001POPTR_0001s00200scaffold_1:12631-13612q1q2NOTEST000011no
P10XLOC_000009POPTR_0001s00360scaffold_1:249046-255958q1q2NOTEST28.5798.77239-1.703911.482290.1382641no
P100XLOC_000087POPTR_0001s02220scaffold_1:1670416-1679146q1q2NOTEST02.428371.79769e+3081.79769e+3080.04163231no
P1000XLOC_000910POPTR_0001s19050scaffold_1:16353426-16359654q1q2NOTEST16.86449.63831.55751-1.442620.1491291no
P10000XLOC_009254POPTR_0012s07910scaffold_12:8901305-8908592q1q2NOTEST7.10274e-058.6807316.8991-0.004845860.9961341no
33: Cuffdiff on data 1, data 2, and data 28: isoform FPKM tracking
45,002 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314151617
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageq1_FPKMq1_conf_loq1_conf_hiq1_statusq2_FPKMq2_conf_loq2_conf_hiq2_status
TCONS_00000001=POPTR_0001s00200.1XLOC_000001POPTR_0001s00200TSS1scaffold_1:12631-13612556-000OK000OK
TCONS_00000002=POPTR_0001s00210.1XLOC_000002POPTR_0001s00210TSS2scaffold_1:19768-22804983-3.739808.05816OK4.4290409.54326OK
TCONS_00000003=POPTR_0001s00220.1XLOC_000003POPTR_0001s00220TSS3scaffold_1:74075-758931071-000OK1.3124203.93727OK
TCONS_00000004=POPTR_0001s00240.1XLOC_000004POPTR_0001s00240TSS4scaffold_1:105027-1079841125-000OK000OK
TCONS_00000005=POPTR_0001s00285.1XLOC_000005POPTR_0001s00285TSS5scaffold_1:154169-155938891-000OK000OK
34: Cuffdiff on data 1, data 2, and data 28: gene FPKM tracking
40,623 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314151617
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageq1_FPKMq1_conf_loq1_conf_hiq1_statusq2_FPKMq2_conf_loq2_conf_hiq2_status
XLOC_000001--XLOC_000001POPTR_0001s00200TSS1scaffold_1:12631-13612--000OK000OK
XLOC_000002--XLOC_000002POPTR_0001s00210TSS2scaffold_1:19768-22804--3.739808.05816OK4.4290409.54326OK
XLOC_000003--XLOC_000003POPTR_0001s00220TSS3scaffold_1:74075-75893--000OK1.3124203.93727OK
XLOC_000004--XLOC_000004POPTR_0001s00240TSS4scaffold_1:105027-107984--000OK000OK
XLOC_000005--XLOC_000005POPTR_0001s00285TSS5scaffold_1:154169-155938--000OK000OK
35: Cuffdiff on data 1, data 2, and data 28: TSS groups FPKM tracking
41,277 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314151617
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageq1_FPKMq1_conf_loq1_conf_hiq1_statusq2_FPKMq2_conf_loq2_conf_hiq2_status
TSS1--XLOC_000001POPTR_0001s00200TSS1scaffold_1:12631-13612--000OK000OK
TSS10--XLOC_000009POPTR_0001s00360TSS10scaffold_1:249046-255958--11.3364025.9829OK000OK
TSS100--XLOC_000096POPTR_0001s02380TSS100scaffold_1:1795537-1797212--14.258029.3472OK28.6509057.6534OK
TSS1000--XLOC_000983POPTR_0001s21340TSS1000scaffold_1:19753744-19759192--4.6214709.54676OK31.4829063.9689OK
TSS10000--XLOC_009844POPTR_0012s05100TSS10000scaffold_12:4588373-4589583--000OK1.5568304.67049OK
36: Cuffdiff on data 1, data 2, and data 28: CDS FPKM tracking
43,828 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314151617
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageq1_FPKMq1_conf_loq1_conf_hiq1_statusq2_FPKMq2_conf_loq2_conf_hiq2_status
P1--XLOC_000001POPTR_0001s00200TSS1scaffold_1:12631-13612--000OK000OK
P10--XLOC_000009POPTR_0001s00360TSS9scaffold_1:249046-255958--28.579059.9654OK8.77239018.9019OK
P100--XLOC_000087POPTR_0001s02220TSS91scaffold_1:1670416-1679146--000OK2.4283705.2324OK
P1000--XLOC_000910POPTR_0001s19050TSS925scaffold_1:16353426-16359654--16.864034.1558OK49.63830103.758OK
P10000--XLOC_009254POPTR_0012s07910TSS9399scaffold_12:8901305-8908592--7.10274e-0500.34345OK8.68073018.0721OK
37: Cuffdiff on data 1, data 2, and data 28: splicing diff
41,277 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314
test_idgene_idgenelocussample_1sample_2statusvalue_1value_2sqrt(JS)test_statp_valueq_valuesignificant
TSS1XLOC_000001POPTR_0001s00200scaffold_1:12631-13612q1q2NOTEST000001no
TSS10XLOC_000009POPTR_0001s00360scaffold_1:249046-255958q1q2NOTEST000001no
TSS100XLOC_000096POPTR_0001s02380scaffold_1:1795537-1797212q1q2NOTEST000001no
TSS1000XLOC_000983POPTR_0001s21340scaffold_1:19753744-19759192q1q2NOTEST000001no
TSS10000XLOC_009844POPTR_0012s05100scaffold_12:4588373-4589583q1q2NOTEST000001no
38: Cuffdiff on data 1, data 2, and data 28: promoters diff
40,623 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314
test_idgene_idgenelocussample_1sample_2statusvalue_1value_2sqrt(JS)test_statp_valueq_valuesignificant
XLOC_000001XLOC_000001POPTR_0001s00200scaffold_1:12631-13612q1q2NOTEST000001no
XLOC_000002XLOC_000002POPTR_0001s00210scaffold_1:19768-22804q1q2NOTEST000001no
XLOC_000003XLOC_000003POPTR_0001s00220scaffold_1:74075-75893q1q2NOTEST000001no
XLOC_000004XLOC_000004POPTR_0001s00240scaffold_1:105027-107984q1q2NOTEST000001no
XLOC_000005XLOC_000005POPTR_0001s00285scaffold_1:154169-155938q1q2NOTEST000001no
39: Cuffdiff on data 1, data 2, and data 28: CDS diff
40,623 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 -b /mnt/spruce/storage/data/sequence/Populus-trichocarpa/v02/Populus_trichocarpa.v2.fa /mnt/spruce/storage/ftp/database/files/003/dataset_3814.dat /mnt/spruce/storage/ftp/database/files/003/da
1234567891011121314
test_idgene_idgenelocussample_1sample_2statusvalue_1value_2sqrt(JS)test_statp_valueq_valuesignificant
XLOC_000001XLOC_000001POPTR_0001s00200scaffold_1:12631-13612q1q2NOTEST000001no
XLOC_000002XLOC_000002POPTR_0001s00210scaffold_1:19768-22804q1q2NOTEST000001no
XLOC_000003XLOC_000003POPTR_0001s00220scaffold_1:74075-75893q1q2NOTEST000001no
XLOC_000004XLOC_000004POPTR_0001s00240scaffold_1:105027-107984q1q2NOTEST000001no
XLOC_000005XLOC_000005POPTR_0001s00285scaffold_1:154169-155938q1q2NOTEST000001no