Matt:LabNotes/2014-8-1
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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: