jla-demultiplexer 0.0.8

Internal lab use tool for 3 end analysis

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