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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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Can trimgalore be used to clean up mate pair libraries? #146

Open gunjanpandey opened 1 year ago

gunjanpandey commented 1 year ago

Wondering if trimgalore can be used to cleanup mate-paired libraries? Is yes, is there a specific flag(s)?

FelixKrueger commented 1 year ago

The standard use case would be single-end or paired-end reads. With mate-paired do you mean a special case of paired-end fragments with a (long) insert size? If so, I am afraid I don't know much about it (it's at least 10 years since I have heard this term...)

gunjanpandey commented 1 year ago

yes, I was wondering if mate-paired, a special case of paired-end fragments with a (long) insert size, could also be cleaned using trimgalore.

FelixKrueger commented 1 year ago

At the end of the day, it looks for a read-through adapter sequence (that typically results from fragments that are shorter than the read length), and trims off low quality base calls. If you think that either of these scenarios are applicable to your experimental setup - I don't see why it wouldn't work. But again, I don't have any experience with it I am afraid.