A collection of useful bioinformatics scripts
Description: Extract alignment statistics from STAR log files.
Language: Python
Usage: starStats.py [-h] -o OUT LOGFILE [LOGFILE ...]
Description: Extract alignment statistics from SAM/BAM files.
Language: Python
Details: Adapted from the Celloline stats script.
More details here.
Usage: alignStats.py [-h] -o OUT [-g GTF] [-i INDEX] -t {sam,bam} [-p PARALLEL] SAM/BAM [SAM/BAM ...]
Description: Download files from SRA using ASCP.
Language: R
Usage: sraDownload.R [-h] [-d DATABASE] [-o OUT] [-a ASCPCMD] [-t TYPE] SRA [SRA ...]
Description: Sample reads from FASTQ files.
Language: R
Usage: sampleFastq [-h] -1 PAIR1 [PAIR1 ...] [-2 [PAIR2 [PAIR2 ...]]] [-n NREADS] [-s SEED] [-o OUTPATH]
Description: Merge FASTQ files based on a filename pattern.
Language: Python
Usage: mergeFastqs [-h] [-s SEPARATOR] [-o OUTDIR] -p PATTERN FASTQ [FASTQ ...]
Description: Run kallisto over multiple FASTQ files.
Language: Python
Usage: kallistoMulti [-h] -i INDEX -o OUTPUT_DIR [-1 READ1 [READ1 ...]] [-2 READ2 [READ2 ...]]
Description: Merge output from multiple kallisto runs.
Language: R
Usage: kallistoMerge [-h] -d DIRECTORY -t TX2GENE [-o OUTPATH]