Matt:LabNotes/2014-8-1: Difference between revisions
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>Mzcai (Created page with "==GenePattern: Tophat & RNA-SeQC== *Using genepattern.broadinstitute.org ===Tophat version 8.6=== *Upload files s_1_1_Indx26.txt s_1_1_Indx27.txt s_1_1_Indx28.txt s_...") |
>Mzcai mNo edit summary |
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*GTF file | *GTF file | ||
Homo_sapiens_GENCODE_hg19_v7_chr1_format.gtf | Homo_sapiens_GENCODE_hg19_v7_chr1_format.gtf | ||
*library type | *library type | ||
Standard Illumina (fr-unstranded) | Standard Illumina (fr-unstranded) | ||
*quality value scale | *quality value scale | ||
Solexa 1.3 (Phred 64) | Solexa 1.3 (Phred 64) | ||
*output prefix | |||
<Indx##reads.pair.1_basename> | |||
*transcriptome only | |||
yes | |||
*'''left blank''': | |||
**transcriptome index | |||
**reads pair 2 | |||
**mate inner distance | |||
**mate std dev | |||
**all others not mentioned were left at default | |||
===RNA-SeQC=== | |||
====Picard.MergeBamAlignment==== | |||
*to add unaligned reads bam file to accepted | |||
====Picard.AddOrReplaceReadGroups==== | |||
*input file: bam | |||
*read group id: | |||
====SortSam==== | |||
*input file: | |||
*sort order: coordinate | |||
output format: BAM | |||
*output prefix: | |||
====SAMtools.FastaIndex==== | |||
*fasta file: reference.fa | |||
*output prefix: | |||
====Picard.CreateSequenceDictionary==== | |||
*reference sequence file: reference.fa | |||
====Picard.ReorderSam==== | |||
*input file: bam/bai pair from SortSam | |||
*reference file: fa/fai from SAMtools.FastaIndex | |||
*reference sequence dictionary: .dict from Picard.CreateSequenceDictionary | |||
====Picard.MarkDuplicates==== | |||
*input file: bam from Picard.ReorderSam | |||
*remove duplicates: no | |||
====SortSam==== | |||
*Update index | |||
*input file: from Picard.MarkDuplicate | |||
*sort order: coordinate | |||
*output: BAM | |||
====RNAseqMetrics==== | |||
*bam files: from SortSam | |||
*sample info file: | |||
*single end: | |||
*annotation gtf: Hg 19, GenCode | |||
*reference sequence: from SAMtools.FastaIndex | |||
*reference sequence index: from SAMtools.FastaIndex | |||
*reference sequence dictionary: from Picard.CreateSequenceDictionary | |||
*num genes: 1000 | |||
*transcript level metrics: no | |||
*gc content file: |
Revision as of 16:38, 8 August 2014
GenePattern: Tophat & RNA-SeQC
- Using genepattern.broadinstitute.org
Tophat version 8.6
- Upload files
s_1_1_Indx26.txt s_1_1_Indx27.txt s_1_1_Indx28.txt s_1_1_Indx29.txt s_1_1_Indx32.txt
- Bowtie index
Homo_sapiens_hg19_UCSC
- GTF file
Homo_sapiens_GENCODE_hg19_v7_chr1_format.gtf
- library type
Standard Illumina (fr-unstranded)
- quality value scale
Solexa 1.3 (Phred 64)
- output prefix
<Indx##reads.pair.1_basename>
- transcriptome only
yes
- left blank:
- transcriptome index
- reads pair 2
- mate inner distance
- mate std dev
- all others not mentioned were left at default
RNA-SeQC
Picard.MergeBamAlignment
- to add unaligned reads bam file to accepted
Picard.AddOrReplaceReadGroups
- input file: bam
- read group id:
SortSam
- input file:
- sort order: coordinate
output format: BAM
- output prefix:
SAMtools.FastaIndex
- fasta file: reference.fa
- output prefix:
Picard.CreateSequenceDictionary
- reference sequence file: reference.fa
Picard.ReorderSam
- input file: bam/bai pair from SortSam
- reference file: fa/fai from SAMtools.FastaIndex
- reference sequence dictionary: .dict from Picard.CreateSequenceDictionary
Picard.MarkDuplicates
- input file: bam from Picard.ReorderSam
- remove duplicates: no
SortSam
- Update index
- input file: from Picard.MarkDuplicate
- sort order: coordinate
- output: BAM
RNAseqMetrics
- bam files: from SortSam
- sample info file:
- single end:
- annotation gtf: Hg 19, GenCode
- reference sequence: from SAMtools.FastaIndex
- reference sequence index: from SAMtools.FastaIndex
- reference sequence dictionary: from Picard.CreateSequenceDictionary
- num genes: 1000
- transcript level metrics: no
- gc content file: