jla-demultiplexer: Internal JLA lab tool for processing gene-specific sequencing experiments
Installation
pip install jla-demultiplexer
Usage
fastqbreakdown: Removes duplicate reads and trims barcodes and randommer addition
fastqbreakdown -r1 [read 1 location] -r2 [read 2 location] \
-r [length of random-mer] -b [barcode]
Notes
- Random-mer length supplied should be 10 or 11
- barcode supplied should be barcode column + gene specific column from manifest
Usage
demultiplexer: Use JLA standard manifests to align and create tail files. Very specific to our gene-specific sequencing methodology
demultiplexer -r1 [read 1 location] -r2 [read 2 location] \
-m [manifest location] -e [ensids] -f [reference fasta]
Notes
- Must provide either -e (comma separated) or -f, but not both
- outputs to location of read 1
- tail file output is compatible with Tailer-Analysis which can be found at https://timnicholsonshaw.shinyapps.io/tailer-analysis/
Usage
jla-trim: Removes duplicate reads and trims randommer addition only. FASTQ output
jla-trim -r1 [read 1 location] -r2 [read 2 location] \
-r [length of random-mer]
Notes
- Random-mer length supplied should be 10 or 11
1 maintainer
Metadata
1 maintainer
Release files for jla-demultiplexer 0.0.8
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