Matt:LabNotes/2014-7-30
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RNA-SeQC
- Bam input
- Add Read Groups and coordinate sort
- Picard.AddOrReplaceReadGroups
- Add Read Groups and coordinate sort
java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.79/AddOrReplaceReadGroups.jar INPUT='accepted_hits.bam' OUTPUT='accepted_hits_RanHex.coorsortRG.bam' SORT_ORDER=coordinate RGID='1' RGLB='RTprimer' RGPL='ILLUMINA' RGPU='flowcell-barcode.lane' RGSM='RanHex'
- Index reference fasta and create sequence dictionary
- reference fasta index already exists
- Index reference fasta and create sequence dictionary
/home/kunzhang/HsGenome/hg19/HsGenome19.fa.fai
- Picard.CreateSequenceDictionary
java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.79/CreateSequenceDictionary.jar REFERENCE=/home/kunzhang/HsGenome/hg19/HsGenome19.fa OUTPUT=/home/mzcai/Genomes/HsGenome19.dict
- Match order of contigs in Bam file to reference file
- Picard.ReorderSam
- Match order of contigs in Bam file to reference file
java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.79/ReorderSam.jar INPUT=accepted_hits_RanHex.coorsortRG.bam OUTPUT=accepted_hits_RanHex.coorsortRGreorder.bam REFERENCE=/home/mzcai/Genomes/HsGenome19.fa
- Index bam file
samtools index accepted_hits_RanHex.coorsortRGreorder.bam
- Create sample file: ~/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_samples.txt
Sample ID Bam File Notes RanHex /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam Indx26RanHex
java -jar /home/kunzhang/softwares/RNA-SeQC_v1.1.7.jar -bwa /home/kunzhang/softwares/bwa-0.7.5a/bwa -BWArRNA /home/mzcai/scratch/RanHex_EnrichmRNA/mart_export_exons_totalrRNA.fa -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output -r /home/mzcai/Genomes/HsGenome19.fa -s /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_samples.txt -singleEnd -t /home/mzcai/LTS/Genomes/Homo_sapiens.GRCh37.75.chr.gtf -ttype 2
The required transcript_id attribute was not found on line chr1 pseudogene gene 11869 14412 . + . gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene";