Question

Can we run FastQC and BWA on .fastq.bz2 files

0

Entering edit mode

8.5 years ago

haiying.kong ▴ 360

Has any one done this? I could try, but the server has been down for several days. :(

sequence • 2.5k views

ADD COMMENT • link updated 21 months ago by Ram 43k • written 8.5 years ago by haiying.kong ▴ 360

score 1 · Answer 1 · 2020-11-17

1

Entering edit mode

3.5 years ago

Carlo Yague 8.7k

Hello, this answer comes a little late but yes, FastQC can read bz2-compressed fastq files directly since 2011. With BWA, you need to uncompress them first, but it can be done in a stream:

bwa mem ref.fa '<bzip2 -dc read1.bz2' '<bzip2 -dc read2.bz2'

ADD COMMENT • link 3.5 years ago by Carlo Yague 8.7k