Mercurial > repos > mingchen0919 > aurora_star_site
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author | mingchen0919 |
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date | Sun, 04 Mar 2018 11:42:48 -0500 |
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--- title: 'STAR: RNA-Seq aligner' output: html_document --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set( echo = as.logical(opt$X_e), error = TRUE ) ``` ## Generating genome indexes ```{bash} cd ${X_d} # create genome directory for genome indexes mkdir -p ${X_d}/genomeDir cat >temp.sh <<EOF STAR \\ --runMode genomeGenerate \\ --genomeDir ${X_d}/genomeDir \\ --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\ --sjdbGTFfile ${X_B} \\ --sjdbOverhang ${X_C} \\ > /dev/null 2>&1 EOF grep -v None temp.sh > index-genome.sh # run star sh index-genome.sh ``` ```{r} # display index-genome code index_genome_sh = paste0(opt$X_d, '/index-genome.sh') tags$code(tags$pre(readChar(index_genome_sh, file.info(index_genome_sh)$size ))) ``` ## Running mapping jobs ```{bash} cd ${X_d} cat >temp.sh <<EOF STAR \\ --genomeDir ${X_d}/genomeDir \\ --readFilesIn \\ ${X_F} \\ ${X_R} \\ > /dev/null 2>&1 EOF grep -v None temp.sh > mapping.sh # run mapping sh mapping.sh ``` ```{r} # display mapping code mapping_sh = paste0(opt$X_d, '/mapping.sh') tags$code(tags$pre(readChar(mapping_sh, file.info(mapping_sh)$size ))) ``` ## SAM to sorted BAM ```{bash} cd ${X_d} echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh sh sam2bam.sh cp Aligned.out.sorted.bam ${X_S} ``` ```{r} # display sam to bam code sam2bam_sh = paste0(opt$X_d, '/sam2bam.sh') tags$code(tags$pre(readChar(sam2bam_sh, file.info(sam2bam_sh)$size ))) ``` ## Mapping statistics ```{bash} cd ${X_d} samtools flagstat Aligned.out.sorted.bam ```