Can we run FastQC and BWA on .fastq.bz2 files
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6.8 years ago
haiying.kong ▴ 360

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

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22 months ago

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'
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