Published Histories | chanaka | Cufflinks Cuffcompare and Cuffdiff
Import history

Galaxy History ' Cufflinks Cuffcompare and Cuffdiff'


DatasetAnnotation
1: Tophat on data 16 and data 15: accepted_hits
5.3 Mb
format: bam, database: Populus_unmasked
Info: TopHat v1.4.1
tophat -p 4 -r 20 /mnt/spruce/storage/data/bowtie_old/nisqually /mnt/spruce/storage/ftp/database/files/003/dataset_3321.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3322.dat
Binary bam alignments file
2: Tophat on data 20 and data 18: accepted_hits
5.2 Mb
format: bam, database: Populus_unmasked
Info: TopHat v1.4.1
tophat -p 4 -r 20 /mnt/spruce/storage/data/bowtie_old/nisqually /mnt/spruce/storage/ftp/database/files/003/dataset_3324.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3326.dat
Binary bam alignments file
3: Cufflinks on data 6: gene expression
484 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
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tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
CUFF.1--CUFF.1--scaffold_1:310854-311392--1152.09658.7641645.41OK
CUFF.2--CUFF.2--scaffold_1:664580-665028--1619.34958.2492280.44OK
CUFF.3--CUFF.3--scaffold_1:3265497-3266132--1683.191170.022196.36OK
CUFF.4--CUFF.4--scaffold_1:3311914-3312400--992.884511.2651474.5OK
CUFF.5--CUFF.5--scaffold_1:3616720-3617081--1356.45604.0262108.87OK
4: Cufflinks on data 6: transcript expression
484 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
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tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
CUFF.1.1--CUFF.1--scaffold_1:310854-3113925385.860051152.09658.7641645.41OK
CUFF.2.1--CUFF.2--scaffold_1:664580-6650284488.236711619.34958.2492280.44OK
CUFF.3.1--CUFF.3--scaffold_1:3265497-32661326358.561481683.191170.022196.36OK
CUFF.4.1--CUFF.4--scaffold_1:3311914-33124004865.05026992.884511.2651474.5OK
CUFF.5.1--CUFF.5--scaffold_1:3616720-36170813616.899511356.45604.0262108.87OK
5: Cufflinks on data 6: assembled transcripts
1,115 lines
format: gtf, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
scaffold_1Cufflinkstranscript3108553113921000..gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "1152.0893866796"; frac "1.030303"; conf_lo "658.763914"; conf_hi "1645.414859"; cov "5.860047";
scaffold_1Cufflinksexon3108553113921000..gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "1152.0893866796"; frac "1.030303"; conf_lo "658.763914"; conf_hi "1645.414859"; cov "5.860047";
scaffold_1Cufflinkstranscript6645816650281000..gene_id "CUFF.2"; transcript_id "CUFF.2.1"; FPKM "1619.3432431655"; frac "1.000000"; conf_lo "958.249132"; conf_hi "2280.437354"; cov "8.236712";
scaffold_1Cufflinksexon6645816650281000..gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "1"; FPKM "1619.3432431655"; frac "1.000000"; conf_lo "958.249132"; conf_hi "2280.437354"; cov "8.236712";
scaffold_1Cufflinkstranscript326549832661321000..gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "1683.1938361727"; frac "1.011628"; conf_lo "1170.024939"; conf_hi "2196.362733"; cov "8.561485";
scaffold_1Cufflinksexon326549832661321000..gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "1683.1938361727"; frac "1.011628"; conf_lo "1170.024939"; conf_hi "2196.362733"; cov "8.561485";
6: Cufflinks on data 8: gene expression
494 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
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tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
CUFF.1--CUFF.1--scaffold_1:112971-113199--4102.261628.56576.02OK
CUFF.2--CUFF.2--scaffold_1:310778-311475--1051.54671.8681431.22OK
CUFF.3--CUFF.3--scaffold_1:664788-665063--3149.271471.664826.89OK
CUFF.4--CUFF.4--scaffold_1:666170-666713--731.551353.781109.32OK
CUFF.5--CUFF.5--scaffold_1:2780065-2780484--844.73335.3391354.12OK
7: Cufflinks on data 8: transcript expression
494 lines
format: tabular, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
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tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageFPKMFPKM_conf_loFPKM_conf_hiFPKM_status
CUFF.1.1--CUFF.1--scaffold_1:112971-11319922820.7964102.261628.56576.02OK
CUFF.2.1--CUFF.2--scaffold_1:310778-3114756975.33071051.54671.8681431.22OK
CUFF.3.1--CUFF.3--scaffold_1:664788-66506327515.96493149.271471.664826.89OK
CUFF.4.1--CUFF.4--scaffold_1:666170-6667135433.70852731.551353.781109.32OK
CUFF.5.1--CUFF.5--scaffold_1:2780065-27804844194.28227844.73335.3391354.12OK
8: Cufflinks on data 8: assembled transcripts
1,137 lines
format: gtf, database: Populus_unmasked
Info: cufflinks v1.3.0
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
scaffold_1Cufflinkstranscript1129721131991000..gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "4102.2611342522"; frac "1.000000"; conf_lo "1628.504593"; conf_hi "6576.017675"; cov "20.796003";
scaffold_1Cufflinksexon1129721131991000..gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "4102.2611342522"; frac "1.000000"; conf_lo "1628.504593"; conf_hi "6576.017675"; cov "20.796003";
scaffold_1Cufflinkstranscript3107793114751000..gene_id "CUFF.2"; transcript_id "CUFF.2.1"; FPKM "1051.5446394494"; frac "1.005376"; conf_lo "671.868172"; conf_hi "1431.221107"; cov "5.330700";
scaffold_1Cufflinksexon3107793114751000..gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "1"; FPKM "1051.5446394494"; frac "1.005376"; conf_lo "671.868172"; conf_hi "1431.221107"; cov "5.330700";
scaffold_1Cufflinkstranscript6647896650631000..gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "3149.2728497813"; frac "1.035714"; conf_lo "1471.657824"; conf_hi "4826.887876"; cov "15.964924";
scaffold_1Cufflinksexon6647896650631000..gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "3149.2728497813"; frac "1.035714"; conf_lo "1471.657824"; conf_hi "4826.887876"; cov "15.964924";
9: Cuffcompare on data 5, data 9, and data 8: 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/001/dataset_1108.dat ./input1 ./input2
# Cuffcompare v1.3.0 | Command line was:
#cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/001/dataset_1108.dat ./input1 ./input2
#
#= Summary for dataset: ./input1 :
# Query mRNAs : 483 in 483 loci (117 multi-exon transcripts)
10: Cuffcompare on data 5, data 9, and data 8: 5 data tmap file
484 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/001/dataset_1108.dat ./input1 ./input2
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ref_gene_idref_idclass_codecuff_gene_idcuff_idFMIFPKMFPKM_conf_loFPKM_conf_hicovlenmajor_iso_idref_match_len
POPTR_0001s00410POPTR_0001s00410.1cCUFF.1CUFF.1.11001152.089387658.7639141645.4148595.860047538CUFF.1.1827
POPTR_0001s00820POPTR_0001s00820.1cCUFF.2CUFF.2.11001619.343243958.2491322280.4373548.236712448CUFF.2.13434
POPTR_0001s04130POPTR_0001s04130.1oCUFF.3CUFF.3.11001683.1938361170.0249392196.3627338.561485635CUFF.3.1180
POPTR_0001s04180POPTR_0001s04180.1cCUFF.4CUFF.4.1100992.884101511.2645691474.5036345.050257486CUFF.4.11737
POPTR_0001s04650POPTR_0001s04650.1cCUFF.5CUFF.5.11001356.448423604.0262172108.8706306.899510361CUFF.5.1858
11: Cuffcompare on data 5, data 9, and data 8: data 5 refmap file
379 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/001/dataset_1108.dat ./input1 ./input2
1234
ref_gene_idref_idclass_codecuff_id_list
POPTR_0001s00410POPTR_0001s00410.1cCUFF.1|CUFF.1.1
POPTR_0001s04180POPTR_0001s04180.1cCUFF.4|CUFF.4.1
POPTR_0001s04650POPTR_0001s04650.1cCUFF.5|CUFF.5.1
POPTR_0001s11010POPTR_0001s11010.1cCUFF.13|CUFF.13.1
POPTR_0001s14260POPTR_0001s14260.1cCUFF.17|CUFF.17.1
12: Cuffcompare on data 5, data 9, and data 8: data 8 tmap file
494 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/001/dataset_1108.dat ./input1 ./input2
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ref_gene_idref_idclass_codecuff_gene_idcuff_idFMIFPKMFPKM_conf_loFPKM_conf_hicovlenmajor_iso_idref_match_len
POPTR_0001s00250POPTR_0001s00250.1cCUFF.1CUFF.1.11004102.2611341628.5045936576.01767520.796003228CUFF.1.12170
POPTR_0001s00410POPTR_0001s00410.1=CUFF.2CUFF.2.11001051.544639671.8681721431.2211075.330700697CUFF.2.1827
POPTR_0001s00820POPTR_0001s00820.1cCUFF.3CUFF.3.11003149.2728501471.6578244826.88787615.964924275CUFF.3.13434
POPTR_0001s00820POPTR_0001s00820.1cCUFF.4CUFF.4.1100731.550751353.7795671109.3219343.708523543CUFF.4.13434
POPTR_0001s03440POPTR_0001s03440.1cCUFF.5CUFF.5.1100844.730112335.3386881354.1215364.282275419CUFF.5.11774
13: Cuffcompare on data 5, data 9, and data 8: data 8 refmap file
397 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/001/dataset_1108.dat ./input1 ./input2
1234
ref_gene_idref_idclass_codecuff_id_list
POPTR_0001s00410POPTR_0001s00410.1=CUFF.2|CUFF.2.1
POPTR_0001s11010POPTR_0001s11010.1cCUFF.15|CUFF.15.1
POPTR_0001s11950POPTR_0001s11950.1cCUFF.16|CUFF.16.1
POPTR_0001s18210POPTR_0001s18210.1cCUFF.19|CUFF.19.1
POPTR_0001s18730POPTR_0001s18730.1cCUFF.20|CUFF.20.1
14: Cuffcompare on data 5, data 9, and data 8: transcript tracking
853 lines
format: tabular, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/001/dataset_1108.dat ./input1 ./input2
123456
TCONS_00000001XLOC_000001POPTR_0001s00410|POPTR_0001s00410.1cq1:CUFF.1|CUFF.1.1|100|1152.089387|658.763914|1645.414859|5.860047|--
TCONS_00000002XLOC_000002POPTR_0001s04130|POPTR_0001s04130.1oq1:CUFF.3|CUFF.3.1|100|1683.193836|1170.024939|2196.362733|8.561485|635q2:CUFF.6|CUFF.6.1|100|2033.719337|1382.407891|2685.030782|10.309737|521
TCONS_00000003XLOC_000003POPTR_0001s04180|POPTR_0001s04180.1cq1:CUFF.4|CUFF.4.1|100|992.884101|511.264569|1474.503634|5.050257|--
TCONS_00000004XLOC_000004POPTR_0001s04650|POPTR_0001s04650.1cq1:CUFF.5|CUFF.5.1|100|1356.448423|604.026217|2108.870630|6.899510|--
TCONS_00000005XLOC_000005POPTR_0001s11010|POPTR_0001s11010.1cq1:CUFF.13|CUFF.13.1|100|1030.129474|481.380361|1578.878587|5.239704|--
TCONS_00000006XLOC_000007POPTR_0001s14260|POPTR_0001s14260.1cq1:CUFF.17|CUFF.17.1|100|991.768151|419.170542|1564.365759|5.044581|--
15: Cuffcompare on data 5, data 9, and data 8: combined transcripts
975 lines
format: gtf, database: Populus_unmasked
Info: cuffcompare v1.3.0 (3022)
cuffcompare -o cc_output -r /mnt/spruce/storage/ftp/database/files/001/dataset_1108.dat ./input1 ./input2
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
scaffold_1Cufflinksexon310779311475.+.gene_id "XLOC_000001"; transcript_id "TCONS_00000060"; exon_number "1"; gene_name "POPTR_0001s00410"; oId "CUFF.2.1"; nearest_ref "POPTR_0001s00410.1"; class_code "="; tss_id "TSS1";
scaffold_1Cufflinksexon32654983266132.+.gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "POPTR_0001s04130"; oId "CUFF.3.1"; nearest_ref "POPTR_0001s04130.1"; class_code "o"; tss_id "TSS2";
scaffold_1Cufflinksexon33119153312400.+.gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "POPTR_0001s04180"; oId "CUFF.4.1"; nearest_ref "POPTR_0001s04180.1"; class_code "c"; tss_id "TSS3";
scaffold_1Cufflinksexon36167213617081.+.gene_id "XLOC_000004"; transcript_id "TCONS_00000004"; exon_number "1"; gene_name "POPTR_0001s04650"; oId "CUFF.5.1"; nearest_ref "POPTR_0001s04650.1"; class_code "c"; tss_id "TSS4";
scaffold_1Cufflinksexon85401428540743.+.gene_id "XLOC_000005"; transcript_id "TCONS_00000061"; exon_number "1"; gene_name "POPTR_0001s11010"; oId "CUFF.15.1"; nearest_ref "POPTR_0001s11010.1"; class_code "c"; tss_id "TSS5";
scaffold_1Cufflinksexon92868999287122.+.gene_id "XLOC_000006"; transcript_id "TCONS_00000062"; exon_number "1"; gene_name "POPTR_0001s11950"; oId "CUFF.16.1"; nearest_ref "POPTR_0001s11950.1"; class_code "c"; tss_id "TSS7";
16: Cuffdiff on data 6, data 8, and data 15: isoform expression
709 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
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test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
TCONS_00000002XLOC_000002POPTR_0001s04130scaffold_1:3265497-3266132q1q2NOTEST4649.094609.79-0.01224690.0395870.9684221no
TCONS_00000003XLOC_000003POPTR_0001s04180scaffold_1:3311914-3312400q1q2NOTEST2540.791001.7-1.342832.074020.03807761no
TCONS_00000004XLOC_000004POPTR_0001s04650scaffold_1:3616720-3617081q1q2NOTEST2549.74994.992-1.357591.423610.1545581no
TCONS_00000006XLOC_000007POPTR_0001s14260scaffold_1:11211550-11212435q1q2NOTEST2080.531055.46-0.979081.175450.2398151no
TCONS_00000007XLOC_000008POPTR_0001s18210scaffold_1:15289559-15289907q1q2NOTEST4906.532074.25-1.242112.287460.02216911no
17: Cuffdiff on data 6, data 8, and data 15: gene expression
461 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
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test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
XLOC_000001XLOC_000001POPTR_0001s00410scaffold_1:310778-311475q1q2NOTEST2296.23203.390.480352-1.241110.2145661no
XLOC_000002XLOC_000002POPTR_0001s04130scaffold_1:3265497-3266132q1q2NOTEST4649.094609.79-0.01224690.0395870.9684221no
XLOC_000003XLOC_000003POPTR_0001s04180scaffold_1:3311914-3312400q1q2NOTEST2540.791001.7-1.342832.074020.03807761no
XLOC_000004XLOC_000004POPTR_0001s04650scaffold_1:3616720-3617081q1q2NOTEST2549.74994.992-1.357591.423610.1545581no
XLOC_000005XLOC_000005POPTR_0001s11010scaffold_1:8540141-8540743q1q2NOTEST1790.022270.210.342848-0.7085180.4786241no
18: Cuffdiff on data 6, data 8, and data 15: TSS groups expression
682 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
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test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
TSS1XLOC_000001POPTR_0001s00410scaffold_1:310778-311475q1q2NOTEST2296.23203.390.480352-1.241110.2145661no
TSS10XLOC_000009POPTR_0001s18730scaffold_1:15868499-15868808q1q2NOTEST1405.143326.541.24331-1.520070.1284931no
TSS100XLOC_000061POPTR_0010s01700scaffold_10:1891719-1892210q1q2NOTEST9482.149732.540.0376037-0.08121030.9352751no
TSS101XLOC_000062POPTR_0010s08670scaffold_10:9563451-9564124q1q2NOTEST2967.513763.560.342848-0.7921470.4282751no
TSS103XLOC_000063POPTR_0010s10140scaffold_10:10710651-10711192q1q2NOTEST2510.512674.540.0913093-0.2025690.8394721no
19: Cuffdiff on data 6, data 8, and data 15: CDS Expression FPKM Tracking
1 line
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
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test_idgene_idgenelocussample_1sample_2statusvalue_1value_2log2(fold_change)test_statp_valueq_valuesignificant
20: Cuffdiff on data 6, data 8, and data 15: isoform FPKM tracking
709 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
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tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverageq1_FPKMq1_conf_loq1_conf_hiq1_statusq2_FPKMq2_conf_loq2_conf_hiq2_status
TCONS_00000002oPOPTR_0001s04130.1XLOC_000002POPTR_0001s04130TSS2scaffold_1:3265497-3266132635-4649.093247.346050.85OK4609.793203.826015.77OK
TCONS_00000003cPOPTR_0001s04180.1XLOC_000003POPTR_0001s04180TSS3scaffold_1:3311914-3312400486-2540.791311.233770.35OK1001.7244.4861758.91OK
TCONS_00000004cPOPTR_0001s04650.1XLOC_000004POPTR_0001s04650TSS4scaffold_1:3616720-3617081361-2549.741135.43964.08OK994.99202188.98OK
TCONS_00000006cPOPTR_0001s14260.1XLOC_000007POPTR_0001s14260TSS8scaffold_1:11211550-11212435403-2080.53879.3373281.73OK1055.4602110.92OK
TCONS_00000007cPOPTR_0001s18210.1XLOC_000008POPTR_0001s18210TSS9scaffold_1:15289559-15289907348-4906.532903.456909.62OK2074.25762.3793386.12OK
21: Cuffdiff on data 6, data 8, and data 15: gene FPKM tracking
461 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
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_0001s00410TSS1scaffold_1:310778-311475--2296.21358.783233.62OK3203.392088.114318.66OK
XLOC_000002--XLOC_000002POPTR_0001s04130TSS2scaffold_1:3265497-3266132--4649.093247.346050.85OK4609.793203.826015.77OK
XLOC_000003--XLOC_000003POPTR_0001s04180TSS3scaffold_1:3311914-3312400--2540.791311.233770.35OK1001.7244.4861758.91OK
XLOC_000004--XLOC_000004POPTR_0001s04650TSS4scaffold_1:3616720-3617081--2549.741135.43964.08OK994.99202188.98OK
XLOC_000005--XLOC_000005POPTR_0001s11010TSS5scaffold_1:8540141-8540743--1790.02895.0122685.04OK2270.211254.943285.48OK
22: Cuffdiff on data 6, data 8, and data 15: TSS groups FPKM tracking
682 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
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_0001s00410TSS1scaffold_1:310778-311475--2296.21358.783233.62OK3203.392088.114318.66OK
TSS10--XLOC_000009POPTR_0001s18730TSS10scaffold_1:15868499-15868808--1405.1402810.27OK3326.541548.435104.65OK
TSS100--XLOC_000061POPTR_0010s01700TSS100scaffold_10:1891719-1892210--9482.145343.7913620.5OK9732.545151.2814313.8OK
TSS101--XLOC_000062POPTR_0010s08670TSS101scaffold_10:9563451-9564124--2967.511640.44294.61OK3763.562258.145268.99OK
TSS103--XLOC_000063POPTR_0010s10140TSS103scaffold_10:10710651-10711192--2510.511387.783633.24OK2674.541507.273841.8OK
23: Cuffdiff on data 6, data 8, and data 15: CDS FPKM tracking
1 line
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
123456789
tracking_idclass_codenearest_ref_idgene_idgene_short_nametss_idlocuslengthcoverage
24: Cuffdiff on data 6, data 8, and data 15: splicing diff
682 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
1234567891011121314
test_idgene_idgenelocussample_1sample_2statusvalue_1value_2sqrt(JS)test_statp_valueq_valuesignificant
TSS1XLOC_000001POPTR_0001s00410scaffold_1:310778-311475q1q2NOTEST000001no
TSS10XLOC_000009POPTR_0001s18730scaffold_1:15868499-15868808q1q2NOTEST000001no
TSS100XLOC_000061POPTR_0010s01700scaffold_10:1891719-1892210q1q2NOTEST000001no
TSS101XLOC_000062POPTR_0010s08670scaffold_10:9563451-9564124q1q2NOTEST000001no
TSS103XLOC_000063POPTR_0010s10140scaffold_10:10710651-10711192q1q2NOTEST000001no
25: Cuffdiff on data 6, data 8, and data 15: promoters diff
461 lines
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
1234567891011121314
test_idgene_idgenelocussample_1sample_2statusvalue_1value_2sqrt(JS)test_statp_valueq_valuesignificant
XLOC_000001XLOC_000001POPTR_0001s00410scaffold_1:310778-311475q1q2NOTEST000001no
XLOC_000002XLOC_000002POPTR_0001s04130scaffold_1:3265497-3266132q1q2NOTEST000001no
XLOC_000003XLOC_000003POPTR_0001s04180scaffold_1:3311914-3312400q1q2NOTEST000001no
XLOC_000004XLOC_000004POPTR_0001s04650scaffold_1:3616720-3617081q1q2NOTEST000001no
XLOC_000005XLOC_000005POPTR_0001s11010scaffold_1:8540141-8540743q1q2NOTEST000001no
26: Cuffdiff on data 6, data 8, and data 15: CDS diff
1 line
format: tabular, database: Populus_unmasked
Info: cuffdiff v1.3.0 (3022)
cuffdiff -q -p 4 -c 1000 --FDR 0.050000 /mnt/spruce/storage/ftp/database/files/003/dataset_3344.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3329.dat /mnt/spruce/storage/ftp/database/files/003/dataset_3331.dat
1234567891011121314
test_idgene_idgenelocussample_1sample_2statusvalue_1value_2sqrt(JS)test_statp_valueq_valuesignificant
27: Filter on data 17
empty
format: tabular, database: Populus_unmasked
Info: Filtering with c14=='yes',
kept 0.00% of 461 lines.
Skipped 1 invalid lines starting at line #1: "test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant"