Galaxy History ' Tophat summary'


DatasetAnnotation
1: Trim sequences on data 10
12.7 Mb
format: fastqsanger, database: ?
Info: Trimming: base 10 to 90
Input: 94055 reads.
Output: 94055 reads.
@SOLEXA14:2:1:10:263#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:12:399#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
2: Trim sequences on data 11
12.7 Mb
format: fastqsanger, database: ?
Info: Trimming: base 10 to 90
Input: 94055 reads.
Output: 94055 reads.
@SOLEXA14:2:1:10:263#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:12:399#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
3: Trim sequences on data 12
12.7 Mb
format: fastqsanger, database: ?
Info: Trimming: base 10 to 90
Input: 93865 reads.
Output: 93865 reads.
@SOLEXA14:2:1:2:1946#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:2:1946#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:3:1703#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
4: Trim sequences on data 13
12.7 Mb
format: fastqsanger, database: ?
Info: Trimming: base 10 to 90
Input: 93865 reads.
Output: 93865 reads.
@SOLEXA14:2:1:2:1946#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:2:1946#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:3:1703#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
5: Tophat on data 16 and data 15: splice junctions
298 regions, 1 comments
format: bed, 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
view in GeneTrack
display in IGB Local Web
1.Chrom2.Start3.End4.Name56.Strand789101112
track name=junctions description="TopHat junctions"
scaffold_3371002610169JUNC000000012+1002610169255,0,0217,250,118
scaffold_15554355554724JUNC000000022-554355554724255,0,0218,240,345
scaffold_15554780555854JUNC000000032-554780555854255,0,0223,190,1055
scaffold_1552485235248680JUNC000000042-52485235248680255,0,0217,250,132
scaffold_1582312078231357JUNC000000056-82312078231357255,0,0224,230,127
6: 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
7: Tophat on data 20 and data 18: splice junctions
290 regions, 1 comments
format: bed, 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
view in GeneTrack
display in IGB Local Web
1.Chrom2.Start3.End4.Name56.Strand789101112
track name=junctions description="TopHat junctions"
scaffold_25251357251524JUNC000000016-251357251524255,0,0223,250,142
scaffold_21412629412772JUNC000000024-412629412772255,0,0224,190,124
scaffold_15452712452862JUNC000000032+452712452862255,0,0221,210,129
scaffold_1534687563468895JUNC000000042-34687563468895255,0,0225,170,122
scaffold_151129085811290989JUNC000000052+1129085811290989255,0,0222,200,111
8: 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
9: imported: Ptrichocarpa_129_gene.gtf
~520,000 lines
format: gtf, database: ?
Info: uploaded Ptrichocarpa_129_gene.gtf
1.Seqname2.Source3.Feature4.Start5.End6.Score7.Strand8.Frame9.Attributes
scaffold_1Ptrichocarpav2_0exon1263212650.+.gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1Ptrichocarpav2_05UTR1263212638.+.gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1Ptrichocarpav2_0CDS1263912650.+0gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1Ptrichocarpav2_0exon1276812891.+.gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1Ptrichocarpav2_0CDS1276812891.+0gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";
scaffold_1Ptrichocarpav2_0exon1311713226.+.gene_name "POPTR_0001s00200"; transcript_id "POPTR_0001s00200.1";