https://github.com/ltla/cruktools

Assorted scripts for running server jobs at CRUK CI
https://github.com/ltla/cruktools

Last synced: about 1 year ago
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Assorted scripts for running server jobs at CRUK CI

• Host: GitHub
• URL: https://github.com/ltla/cruktools
• Owner: LTLA
• Created: 2017-10-11T17:43:12.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2019-01-19T13:35:58.000Z (over 7 years ago)
• Last Synced: 2025-02-10T12:29:11.177Z (over 1 year ago)
• Language: Shell
• Size: 20.5 KB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# CRUK tools

This repository provides some tools for processing genomics data on the CRUK Cambridge Institute SLURM server.

**Alignment**

- `solo_align.sh` provides a script for aligning a single library (single-end or paired-end).

- `multi_align.sh` is a convenience wrapper to submit alignment jobs for many libraries in a data set.

- `guess_encoding.py` guesses the Phred encoding for the aligner.

Alignment is performed using the [_subread_](http://subread.sourceforge.net/) aligner.

It also requires [_samtools_](http://www.htslib.org/) and [_MarkDuplicates_](https://broadinstitute.github.io/picard/).

**Read counting**

`counter.R` provides a template for read counting to produce a gene-by-sample count matrix.

It requires specification of the BAM files for which to perform the counting as well as a set of GTF annotation files.

It will use the `featureCounts` function in the [_Rsubread_](https://bioconductor.org/packages/Rsubread) package.

**Data mangling**

- `cram2fastq.sh` will convert a CRAM file into FASTQ for entry into the alignment pipelines above.

- `sanger_dump.sh` will convert an entire folder of CRAM files into FASTQs.

**Other**

`cell_ranger.sh` will call the [_CellRanger_](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) pipeline to create a count matrix for single-cell transcriptomics data from the 10X Genomics platform.