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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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adapter regular expression #40

Closed wangjiawen2013 closed 5 years ago

wangjiawen2013 commented 5 years ago

Dear, There are two adapters in my fastq (CATG/ TGCA) , can I remove them with regular expression CATG|TGCA ?

FelixKrueger commented 5 years ago

I am afraid this is not possible within Trim Galore, but you would have to run two consecutive runs.

wangjiawen2013 commented 5 years ago

I am afraid this is not possible within Trim Galore, but you would have to run two consecutive runs.

the adapter sequence is CATG, but I find the sequence that don't have CATG are also cut. I don't know why. Are the adapter too short ? here is the code: trim_galore --paired --dont_gzip --adapter CATG --adapter2 CATG --length 6 --fastqc --stringency 4 -e 0 rawdata/LR01_R1_promoter.fq rawdata/LR01_R2_promoter.fq

FelixKrueger commented 5 years ago

Hmm, to me it looks like his command would try to find CATG in Read 1, and CATG again in Read 2 (why not leave out --adapter2 then?) if the sequence is fully present in the sequence. In addition, sequences would also be quality trimmed with a Phred threshold of 20.

wangjiawen2013 commented 5 years ago

Good advice, thanks!