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czbiohub-sf / rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
http://nf-co.re
MIT License
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Support gencode GTF files #11

Closed olgabot closed 5 years ago

olgabot commented 5 years ago

Specifically for counting gene biotypes:

    # NOTE: ENSEMBL uses "gene_biotype" while vs GENCODE uses "gene_type"
    htseq-count --order pos \
      --stranded ${strandedness} \
      --idattr gene_biotype \
      --mode union \
      --nonunique all \
      --format bam \
      ${bam_htseqcount} \
      ${gtf} \
      > ${bam_htseqcount.baseName}_biotype.htseq-count.txt
olgabot commented 5 years ago

Closed by https://github.com/czbiohub/rnaseq/pull/15