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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
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md5sum #182

Closed zhangqc723 closed 9 months ago

zhangqc723 commented 10 months ago

I run TrimGalore twice as follow code, trim_galore \ --cores 8 --quality 20 --stringency 3 \ --paired --phred33 \ --output_dir /test \ R1.fq.gz R2.fq.gz And I view the md5 value of output from same R1 and R2 file, but the value is different. Could you tell me why? Thanks!

FelixKrueger commented 9 months ago

My guess is that this has to do with the gzip compression, together with the--cores 8. If trimmed sequences get reported in a different order due to multi-core processing, the compressed files do not necessarily have the same file size.