GDC Base Template

Contains dockerfile and HTSeq utility tools for running the GDC HTSeq expression quantification workflows. See https://github.com/NCI-GDC/htseq-cwl for more information about the GDC workflow associated with this.

Usage

gene_lengths

Generate the gene exon lengths from GTF for use in normalization.

usage: htseq-tools gene_lengths [-h] --gtf_file GTF_FILE --out_file OUT_FILE

Extract gene exon lengths from GTF

optional arguments:
  -h, --help           show this help message and exit
  --gtf_file GTF_FILE  GTF file used for htseq count
  --out_file OUT_FILE  Output TSV file to write to

merge_counts

When an aliquot has a mixture of paired- and single-end, this will merge the counts to a single file.

usage: htseq-tools merge_counts [-h] --htseq_counts HTSEQ_COUNTS --out_file
                                OUT_FILE

Merge PE and SE counts from HTseq

optional arguments:
  -h, --help            show this help message and exit
  --htseq_counts HTSEQ_COUNTS
                        HTSeq count file. Use multiple times
  --out_file OUT_FILE   Output TSV file to write to

fpkm

Normalize the raw counts using the FPKM and FPKM-UQ methods.

usage: htseq-tools fpkm [-h] --aggregate_length_file AGGREGATE_LENGTH_FILE
                        --htseq_counts HTSEQ_COUNTS --output_prefix
                        OUTPUT_PREFIX

Get FPKM and FPKM-UQ

optional arguments:
  -h, --help            show this help message and exit
  --aggregate_length_file AGGREGATE_LENGTH_FILE
                        Aggregate length TSV
  --htseq_counts HTSEQ_COUNTS
                        HTSeq counts txt file
  --output_prefix OUTPUT_PREFIX
                        The output prefix to use.