search

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
459 stars 149 forks source link

md5sum #182

Closed zhangqc723 closed 7 months ago

zhangqc723 commented 7 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 7 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.