Appendix: Parameters of external tools

This page lists the parameters (command-line options) that cgpRna (version: 2.3.0) uses when running external tools below.

• STAR (Version 2.5.0c) mapping:

   STAR --runMode alignReads \
   --sjdbOverhang 99 \
   --limitBAMsortRAM 64606632121 \
   --limitSjdbInsertNsj 1000000 \
   --outSAMtype BAM Unsorted \
   --outSAMstrandField intronMotif \
   --outSAMattributes NH HI NM MD AS XS \
   --outSAMunmapped Within \
   --outSAMheaderHD @HD VN:1.4 SO:unsorted \
   --outFilterMultimapNmax 20 \
   --outFilterScoreMinOverLread 0.33 \
   --outFilterIntronMotifs RemoveNoncanonicalUnannotated \
   --alignIntronMax 200000 \
   --alignMatesGapMax 200000 \
   --alignSJDBoverhangMin 1 \
   --quantMode TranscriptomeSAM \
   --readFilesCommand zcat \
   --outSAMheaderCommentFile ${OUT_COMMENT_FILE} \
   --outSAMattrRGline ${CUSTOM_RG_LINE} \
   --outFileNamePrefix ${OUTPUT_DIR} \
   --runThreadN ${THREADS} \
   --genomeDir ${REFERENCE_DIR} \
   --sjdbGTFfile ${TRANSCRIPTOME_GTF_FILE} \
   --readFilesIn ${GZIPPED_FASTQ_1} ${GZIPPED_FASTQ_2}

• HTSeq-count (Version 0.7.2):

   htseq-count \
   --format=bam \
   --order=name \
   --stranded="no" \
   --type="exon" \
   --idattr="gene_id" \
   --mode="union" \
   --quiet \
   $OUTDIR/tmpCollated.bam ${HTSEQ_GTF}