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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 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:TotoRNAseq_on_130120_HL141] ==Low-level data processing of HL141_2 RNAseq data== *The same flowcell was repeated because one sequencing primer was not used by accident in the first run. cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx01.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx01.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx01_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx03.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx03.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx03_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx04.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx04.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx04_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx06.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx06.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx06_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx07.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx07.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx07_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx09.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx09.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx09_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx10.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx10.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx10_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx11.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx11.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx11_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx12.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx12.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx12_sequence.txt & cat /home/kunzhang/seqStore/130123_HL141_2/s_1_1_Indx13.txt /home/kunzhang/seqStore/130123_HL141_2/s_5_1_Indx13.txt | /home/kunzhang/RNAseq/Data/fastq_tso_r02.pl > Indx13_sequence.txt & *After removing TSOs, read trimming, tophat mapping and extraction of transcript abundance was carried out using a [[Media: RL_HBR_HL141_2_batch_processing.txt |batch processing script]].
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