Galaxy History ' RSEM V156'


DatasetAnnotation
1: asp5_leaf_read2.P001.fq
136.7 Mb
format: fastqsanger, database: Populus_unmasked
Info: Aspen leaves paired-end reads (2 into 50 bp) and the target insert size was 200 bp.
@SOLEXA14:5:1:1:1424#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:1:1424#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:2:1420#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
2: asp5_leaf_read1.P001.fq
136.7 Mb
format: fastqsanger, database: Populus_unmasked
Info: Aspen leaves paired-end reads (2 into 50 bp) and the target insert size was 200 bp.
@SOLEXA14:5:1:1:1424#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:1:1424#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:2:1420#0/1
CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
3: asp5_xylem_read1.P001.fq
142.5 Mb
format: fastqsanger, database: Populus_unmasked
Info: Aspen xylem paired-end reads (2 into 50 bp) and the target insert size was 200 bp.
@SOLEXA14:2:1:1:234#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:1:234#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:2:1946#0/1
CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
4: asp5_xylem_read2.P001.fq
142.5 Mb
format: fastqsanger, database: Populus_unmasked
Info: Aspen xylem paired-end reads (2 into 50 bp) and the target insert size was 200 bp.
@SOLEXA14:2:1:1:234#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:1:234#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:2:1946#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
5: PopGenIE random fastq extract tool on data 2 and data 1
13.7 Mb
format: fastqsanger, database: Populus_unmasked
@SOLEXA14:5:1:9:590#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:9:590#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:15:677#0/2
CCCACTTCTGTTCTTTGTCTTTTCCNNCNAANCNNNNNNNNNNNNNNNNNN
6: PopGenIE random fastq extract tool on data 2 and data 1
13.7 Mb
format: fastqsanger, database: Populus_unmasked
@SOLEXA14:5:1:9:590#0/1
AGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:9:590#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:15:677#0/1
CACTCCAATGATCGAGATATTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNN
7: PopGenIE random fastq extract tool on data 4 and data 3
14.2 Mb
format: fastqsanger, database: Populus_unmasked
@SOLEXA14:2:1:10:263#0/1
TGGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:11:1729#0/1
TTACGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
8: PopGenIE random fastq extract tool on data 4 and data 3
14.2 Mb
format: fastqsanger, database: Populus_unmasked
@SOLEXA14:2:1:10:263#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:11:1729#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
9: FASTQ Groomer on data 5
13.7 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 89984 sanger reads into sanger reads.
Based upon quality and sequence, the input data is valid for: solexa, sanger, illumina
Input ASCII range: 'B'(66) - 'h'(104)
Input decimal range: 33 - 71
@SOLEXA14:5:1:9:590#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:9:590#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:15:677#0/2
CCCACTTCTGTTCTTTGTCTTTTCCNNCNAANCNNNNNNNNNNNNNNNNNN
10: FASTQ Groomer on data 6
13.7 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 89984 sanger reads into sanger reads.
Based upon quality and sequence, the input data is valid for: solexa, sanger, illumina
Input ASCII range: 'B'(66) - 'h'(104)
Input decimal range: 33 - 71
@SOLEXA14:5:1:9:590#0/1
AGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:9:590#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:15:677#0/1
CACTCCAATGATCGAGATATTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNN
11: FASTQ Groomer on data 7
14.2 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 93742 sanger reads into sanger reads.
Based upon quality and sequence, the input data is valid for: solexa, sanger, illumina
Input ASCII range: 'B'(66) - 'h'(104)
Input decimal range: 33 - 71
@SOLEXA14:2:1:10:263#0/1
TGGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:11:1729#0/1
TTACGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
12: FASTQ Groomer on data 8
14.2 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 93742 sanger reads into sanger reads.
Based upon quality and sequence, the input data is valid for: solexa, sanger, illumina
Input ASCII range: 'B'(66) - 'h'(104)
Input decimal range: 33 - 71
@SOLEXA14:2:1:10:263#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:11:1729#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
13: Trim sequences on data 9
12.1 Mb
format: fastqsanger, database: Populus_unmasked
Info: Trimming: base 10 to 90
Input: 89984 reads.
Output: 89984 reads.
@SOLEXA14:5:1:9:590#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:9:590#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:15:677#0/2
GTTCTTTGTCTTTTCCNNCNAANCNNNNNNNNNNNNNNNNNN
14: Trim sequences on data 10
12.1 Mb
format: fastqsanger, database: Populus_unmasked
Info: Trimming: base 10 to 90
Input: 89984 reads.
Output: 89984 reads.
@SOLEXA14:5:1:9:590#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:5:1:9:590#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:5:1:15:677#0/1
GATCGAGATATTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNN
15: Trim sequences on data 11
12.6 Mb
format: fastqsanger, database: Populus_unmasked
Info: Trimming: base 10 to 90
Input: 93742 reads.
Output: 93742 reads.
@SOLEXA14:2:1:10:263#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:11:1729#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
16: Trim sequences on data 12
12.6 Mb
format: fastqsanger, database: Populus_unmasked
Info: Trimming: base 10 to 90
Input: 93742 reads.
Output: 93742 reads.
@SOLEXA14:2:1:10:263#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SOLEXA14:2:1:10:263#0/2
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SOLEXA14:2:1:11:1729#0/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
17: .gene_abundances
40,668 lines
format: tabular, database: Populus_unmasked
1234
POPTR_0001s002000.000POPTR_0001s00200.1
POPTR_0001s002100.215.0600589178051e-06POPTR_0001s00210.1
POPTR_0001s002200.000POPTR_0001s00220.1
POPTR_0001s002300.000POPTR_0001s00230.1
POPTR_0001s002400.000POPTR_0001s00240.1
POPTR_0001s002505.675.82319379940464e-05POPTR_0001s00250.1
18: .isoform_abundances
45,012 lines
format: tabular, database: Populus_unmasked
1234
POPTR_0001s00200.10.000POPTR_0001s00200
POPTR_0001s00210.10.215.0600589178051e-06POPTR_0001s00210
POPTR_0001s00220.10.000POPTR_0001s00220
POPTR_0001s00230.10.000POPTR_0001s00230
POPTR_0001s00240.10.000POPTR_0001s00240
POPTR_0001s00250.15.675.82319379940464e-05POPTR_0001s00250
19: .transcript.bam
7.1 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
20: .rsem_log
10 lines
format: txt, database: Populus_unmasked
RSEM Parameters used by Galaxy:
/usr/local/bin/rsem-calculate-expression --quiet --paired-end -p 1 --forward-prob 0.5 --seed-length 25 --bowtie-n 2 --bowtie-e 99999999 --bowtie-m 200 --fragment-length-mean -1 --phred33-quals /mnt/spruce/storage/ftp/database/files/002/dataset_2529.dat /mn
t/spruce/storage/ftp/database/files/002/dataset_2530.dat /mnt/spruce/storage/data/rsem/populus_156/Populus_156 /mnt/spruce/storage/ftp/database/files/002/dataset_2533.dat
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 1 -a -m 200 -S --quiet /mnt/spruce/storage/data/rsem/populus_156/Populus_156 -1 /mnt/spruce/storage/ftp/database/files/002/dataset_2529.dat -2 /mnt/spruce/storage/ftp/database/files/002/datas
et_2530.dat | gzip > /mnt/spruce/storage/ftp/database/files/002/dataset_2533.dat.sam.gz
21: .gene_abundances
40,668 lines
format: tabular, database: Populus_unmasked
1234
POPTR_0001s002000.000POPTR_0001s00200.1
POPTR_0001s002100.000POPTR_0001s00210.1
POPTR_0001s002200.000POPTR_0001s00220.1
POPTR_0001s002300.000POPTR_0001s00230.1
POPTR_0001s002400.000POPTR_0001s00240.1
POPTR_0001s0025023.920.000265320121389404POPTR_0001s00250.1
22: .isoform_abundances
45,012 lines
format: tabular, database: Populus_unmasked
1234
POPTR_0001s00200.10.000POPTR_0001s00200
POPTR_0001s00210.10.000POPTR_0001s00210
POPTR_0001s00220.10.000POPTR_0001s00220
POPTR_0001s00230.10.000POPTR_0001s00230
POPTR_0001s00240.10.000POPTR_0001s00240
POPTR_0001s00250.123.920.000265320121389404POPTR_0001s00250
23: .transcript.bam
6.8 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
24: .rsem_log
10 lines
format: txt, database: Populus_unmasked
RSEM Parameters used by Galaxy:
/usr/local/bin/rsem-calculate-expression --quiet --paired-end -p 1 --forward-prob 0.5 --seed-length 25 --bowtie-n 2 --bowtie-e 99999999 --bowtie-m 200 --fragment-length-mean -1 --phred33-quals /mnt/spruce/storage/ftp/database/files/002/dataset_2531.dat /mn
t/spruce/storage/ftp/database/files/002/dataset_2532.dat /mnt/spruce/storage/data/rsem/populus_156/Populus_156 /mnt/spruce/storage/ftp/database/files/002/dataset_2537.dat
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 1 -a -m 200 -S --quiet /mnt/spruce/storage/data/rsem/populus_156/Populus_156 -1 /mnt/spruce/storage/ftp/database/files/002/dataset_2531.dat -2 /mnt/spruce/storage/ftp/database/files/002/datas
et_2532.dat | gzip > /mnt/spruce/storage/ftp/database/files/002/dataset_2537.dat.sam.gz