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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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option --length might not working got v0.4.5_dev #24

Closed lufuhao closed 6 years ago

lufuhao commented 6 years ago

hi, I used "--length 70" for mate pairs, but still many reads shorter than 70 go to final output.

Would you please double check?

FelixKrueger commented 6 years ago

Which version of Trim Galore were you using? I just tried 1 million reads of a random paired-end 2x125 bp data set (SRR6129181) and ran the following command:

trim_galore --paired --length 70 R1.fastq.gz R2.fastq.gz

All of the resulting trimmed reads come back with a read length between 70-125bp, according to FastQC.