Kun:LabNotes/SingleCellExpr/2013-1-23

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Low-level data processing of HL141 RNAseq data

  • The libraries were made by Rui:LabNotes/SingleCell/2013-1-15.
  • Only one of the two sequencing primers were used by accident, so we have data only for the libraries based on the SMARTer TSO(Indx02,05,08)
  • For these libraries, the barcodes are simply the standard Illumina N2 barcodes. For adapter removal, I simply trimmed the first 10 bases.
  cat /home/kunzhang/seqStore/130120_HL141/s_1_1_Indx02.txt /home/kunzhang/seqStore/130120_HL141/s_5_1_Indx02.txt | trimFastq.pl 10 27 > Indx02_trimmed.txt &
  cat /home/kunzhang/seqStore/130120_HL141/s_1_1_Indx05.txt /home/kunzhang/seqStore/130120_HL141/s_5_1_Indx05.txt | trimFastq.pl 10 27 > Indx05_trimmed.txt &
  cat /home/kunzhang/seqStore/130120_HL141/s_1_1_Indx08.txt /home/kunzhang/seqStore/130120_HL141/s_5_1_Indx08.txt | trimFastq.pl 10 27 > Indx08_trimmed.txt &
  nohup tophat2 -p 2 --transcriptome-index=/home/kunzhang/RNAseq/Data/CommonFiles/tophat_transcriptome_index/gencode14 --library-type fr-secondstrand --solexa1.3-quals -o Indx02 /GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome Indx02_trimmed.txt > Indx02.tophat.log&
  nohup tophat2 -p 2 --transcriptome-index=/home/kunzhang/RNAseq/Data/CommonFiles/tophat_transcriptome_index/gencode14 --library-type fr-secondstrand --solexa1.3-quals -o Indx05 /GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome Indx05_trimmed.txt > Indx05.tophat.log&
  nohup tophat2 -p 2 --transcriptome-index=/home/kunzhang/RNAseq/Data/CommonFiles/tophat_transcriptome_index/gencode14 --library-type fr-secondstrand --solexa1.3-quals -o Indx08 /GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome Indx08_trimmed.txt > Indx08.tophat.log&
 nohup /home/kunzhang/softwares/cufflinks-latest/cufflinks -G /home/kunzhang/RNAseq/Data/CommonFiles/gencode.v14.annotation.gtf -p 4 --library-type fr-secondstrand -o Indx02 Indx02/accepted_hits.bam > Indx02.cufflink.log&
 nohup /home/kunzhang/softwares/cufflinks-latest/cufflinks -G /home/kunzhang/RNAseq/Data/CommonFiles/gencode.v14.annotation.gtf -p 4 --library-type fr-secondstrand -o Indx05 Indx05/accepted_hits.bam > Indx05.cufflink.log&
 nohup /home/kunzhang/softwares/cufflinks-latest/cufflinks -G /home/kunzhang/RNAseq/Data/CommonFiles/gencode.v14.annotation.gtf -p 4 --library-type fr-secondstrand -o Indx08 Indx08/accepted_hits.bam > Indx08.cufflink.log&
  • Following analysis is on [1]