rageseq

RAGE-seq scripts

Barcode extraction

Demultiplexing

rageMatch.py

Used to read the barcode whitelist, search the total fastq, bin reads on barcode matches, and trim to poly TAil.

Used on an HPC environment with Sun Grid Engine

sge:

source ~/venv2714/bin/activate
time python rageMatch.py -q ramos.fastq.gz -b Ramos_master_barcodes.tsv -n ${SGE_TASK_ID} -c 4000 -t 10 -o ${TMPDIR}/ramos -l 0 -f 250 -s
cp ${TMPDIR}/ramos/* ./ramos/output

Command:

LINES=$(wc -l Ramos_master_barcodes.tsv | awk '{print $1}')

CMD="qsub -cwd -V -pe smp 1 -N R_DM -S /bin/bash -t 1-$LINES -l mem_requested=8G,h_vmem=8G,tmp_requested=50G ../rageMatch.sge"
echo $CMD && $CMD

usage: rageMatch.py [-h] [-q FASTQ] [-o OUTPUT] [-b BARCODES]
                    [-n BARCODENUMBER] [-c CHUNKS] [-l LENGTH] [-f FILTER]
                    [-t TRIM] [-v] [-s]

rageMatch - RageSeq direct matching and trimming

optional arguments:
  -h, --help            show this help message and exit
  -q FASTQ, --fastq FASTQ
                        fastq file - gzipped
  -o OUTPUT, --output OUTPUT
                        barcode fastq output prefix
  -b BARCODES, --barcodes BARCODES
                        barcode file - built from transform_bc.py
  -n BARCODENUMBER, --barcodeNumber BARCODENUMBER
                        The barcode line number from the barcode file 1
                        indexed - used for HPC array jobs or a single barcode
  -c CHUNKS, --chunks CHUNKS
                        Number of reads to store in memory before processing
  -l LENGTH, --length LENGTH
                        Number of nt to search at start and end
  -f FILTER, --filter FILTER
                        Min length of read required to be used
  -t TRIM, --trim TRIM  Trim barcodes and adapters from reads - number of
                        bases
  -v, --verbose         Engage higher output verbosity
  -s, --stats           dump match stats into header

Assebmly

See our preprint:

https://www.biorxiv.org/content/early/2018/09/24/424945