https://github.com/lazappi/binf-scripts
A collection of useful bioinformatics scripts.
https://github.com/lazappi/binf-scripts
bioinformatics bioinformatics-scripts
Last synced: 10 months ago
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A collection of useful bioinformatics scripts.
- Host: GitHub
- URL: https://github.com/lazappi/binf-scripts
- Owner: lazappi
- License: mit
- Created: 2016-03-30T02:46:37.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2016-12-13T04:14:31.000Z (over 9 years ago)
- Last Synced: 2025-04-14T21:24:20.039Z (about 1 year ago)
- Topics: bioinformatics, bioinformatics-scripts
- Language: Python
- Homepage:
- Size: 27.3 KB
- Stars: 8
- Watchers: 2
- Forks: 7
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
My bioinformatics scripts
=========================
A collection of useful bioinformatics scripts
starStats.py
------------
**Description:** Extract alignment statistics from STAR log files.
**Language:** Python
**Usage:** `starStats.py [-h] -o OUT LOGFILE [LOGFILE ...]`
alignStats.py
-------------
**Description:** Extract alignment statistics from SAM/BAM files.
**Language:** Python
**Details:** Adapted from the `Celloline` [stats script](https://github.com/Teichlab/celloline/blob/master/lib/stats.py).
More details [here](http://lazappi.id.au/extracting-alignment-statistics-using-python/).
**Usage**: `alignStats.py [-h] -o OUT [-g GTF] [-i INDEX] -t {sam,bam}
[-p PARALLEL] SAM/BAM [SAM/BAM ...]`
sraDownload.R
-------------
**Description:** Download files from SRA using ASCP.
**Language:** R
**Usage:** `sraDownload.R [-h] [-d DATABASE] [-o OUT] [-a ASCPCMD] [-t TYPE]
SRA [SRA ...]`
sampleFastq.R
-------------
**Description:** Sample reads from FASTQ files.
**Language:** R
**Usage:** `sampleFastq [-h] -1 PAIR1 [PAIR1 ...] [-2 [PAIR2 [PAIR2 ...]]]
[-n NREADS] [-s SEED] [-o OUTPATH]`
mergeFastqs.py
-------------
**Description:** Merge FASTQ files based on a filename pattern.
**Language:** Python
**Usage:** `mergeFastqs [-h] [-s SEPARATOR] [-o OUTDIR] -p PATTERN FASTQ
[FASTQ ...]`
kallistoMulti.py
----------------
**Description:** Run kallisto over multiple FASTQ files.
**Language:** Python
**Usage:** `kallistoMulti [-h] -i INDEX -o OUTPUT_DIR [-1 READ1 [READ1 ...]]
[-2 READ2 [READ2 ...]]`
kallistoMerge.R
---------------
**Description:** Merge output from multiple kallisto runs.
**Language:** R
**Usage:** `kallistoMerge [-h] -d DIRECTORY -t TX2GENE [-o OUTPATH]`