https://github.com/nci-gdc/htseq-tool

Utility scripts for processing HTSeq counts data
https://github.com/nci-gdc/htseq-tool

bioinformatics docker workflow-tool

Last synced: 3 months ago
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Utility scripts for processing HTSeq counts data

• Host: GitHub
• URL: https://github.com/nci-gdc/htseq-tool
• Owner: NCI-GDC
• License: apache-2.0
• Created: 2016-01-07T18:59:27.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2023-03-29T19:17:02.000Z (about 3 years ago)
• Last Synced: 2025-09-05T13:51:20.268Z (10 months ago)
• Topics: bioinformatics, docker, workflow-tool
• Language: Python
• Homepage:
• Size: 374 KB
• Stars: 3
• Watchers: 9
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
# GDC Base Template

![Version badge](https://img.shields.io/badge/htslib-1.8-.svg)

![Version badge](https://img.shields.io/badge/samtools-1.8-.svg)

![Version badge](https://img.shields.io/badge/HTSeq-0.6.1p1-.svg)

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.

```