Skip to content

Instantly share code, notes, and snippets.

@standage

standage/norm-2014-09-17.sh

Created September 17, 2014 20:37
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save standage/4222de94bd695f23f673 to your computer and use it in GitHub Desktop.
Save standage/4222de94bd695f23f673 to your computer and use it in GitHub Desktop.
Download ZIP
Seems to have issues with khmer 1.1
Raw
norm-2014-09-17.sh
#!/usr/bin/env bash
set -e
which fastq-dump # http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
which interleave-reads.py
which normalize-by-median.py
curl -O ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR494/SRR494178/SRR494178.sra
fastq-dump --split-files SRR494178.sra
interleave-reads.py SRR494178_1.fastq SRR494178_2.fastq -o SRR494178_int.fastq
normalize-by-median.py -k 17 -p -N 4 -x 8e9 SRR494178_int.fastq
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment