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Galaxy History ' Send Data to Popgenie'

Dataset

Annotation

3: View data in Popgenie GBrowse

200 lines
format: gtf, database: Populus_unmasked

1.Seqname 2.Source 3.Feature 4.Start 5.End 6.Score 7.Strand 8.Frame 9.Attributes
scaffold_1 Ptrichocarpav2_0 exon 12632 12650 . + . gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1 Ptrichocarpav2_0 5UTR 12632 12638 . + . gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1 Ptrichocarpav2_0 CDS 12639 12650 . + 0 gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1 Ptrichocarpav2_0 exon 12768 12891 . + . gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1 Ptrichocarpav2_0 CDS 12768 12891 . + 0 gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1 Ptrichocarpav2_0 exon 13117 13226 . + . gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";

None

4: Sample output from RNASeq Analysis

100 lines
format: tabular, database: Populus_unmasked

1
POPTR_0001s04350
POPTR_0001s28170
POPTR_0001s35530
POPTR_0001s45510
POPTR_0001s10980
POPTR_0001s30020

None

5: Cuffdiff on data 14, data 16, and data 29: gene expression

9,193 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/001/dataset_1092.dat /mnt/spruce/storage/ftp/database/files/001/dataset_1077.dat /mnt/spruce/storage/ftp/database/files/001/dataset_1079.dat

1 2 3 4 5 6 7 8 9 10 11 12 13 14
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
XLOC_000001 XLOC_000001 POPTR_0001s00300 scaffold_1:168837-170022 q1 q2 NOTEST 23.6144 108.106 2.19471 -1.28611 0.198404 1 no
XLOC_000002 XLOC_000002 POPTR_0001s00360 scaffold_1:251869-255906 q1 q2 NOTEST 39.1898 261.222 2.73672 -1.82573 0.0678914 1 no
XLOC_000003 XLOC_000003 POPTR_0001s00390 scaffold_1:303224-303505 q1 q2 NOTEST 55.2562 478.569 3.11452 -1.16674 0.243315 1 no
XLOC_000004 XLOC_000004 POPTR_0001s00410 scaffold_1:310597-311584 q1 q2 NOTEST 3.75577 1144.71 8.25165 -3.1009 0.00192935 1 no
XLOC_000005 XLOC_000005 POPTR_0001s00500 scaffold_1:399099-399507 q1 q2 NOTEST 16.3293 140.167 3.10161 -1.15669 0.247399 1 no

6: Cut on data 5

9,193 lines
format: tabular, database: Populus_unmasked

1
gene
POPTR_0001s00300
POPTR_0001s00360
POPTR_0001s00390
POPTR_0001s00410
POPTR_0001s00500

7: Select first on data 6

1,000 lines
format: tabular, database: Populus_unmasked

1
gene
POPTR_0001s00300
POPTR_0001s00360
POPTR_0001s00390
POPTR_0001s00410
POPTR_0001s00500

8: Select first on data 7

100 lines
format: tabular, database: Populus_unmasked

1
gene
POPTR_0001s00300
POPTR_0001s00360
POPTR_0001s00390
POPTR_0001s00410
POPTR_0001s00500

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Galaxy History ' Send Data to Popgenie'

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