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GeorgetteTanner / w-Wessim2

A tool for in silico whole-exome sequencing.
GNU General Public License v3.0
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Question: specification of read length #1

Closed ajw2329 closed 1 year ago

ajw2329 commented 1 year ago

Hello and thanks for the great tool! I have a quick question: is it possible to specify the read length directly for paired-end output (as opposed to just the fragment length distribution)? It looks like it is hardcoded to 180 -- am I reading that right? Would appreciate any help -- thanks!

GeorgetteTanner commented 1 year ago

Hello

Thanks for your interest in w-Wessim2. The read lengths are taken from the ReSeq error profiles and so it's not possible to directly specify a read length. But if needed, you could train a new ReSeq error profile using reads of the required length.
(The 180 in the code just sets a maximum length for when writing the intermediate read sequences, which are then passed to ReSeq and cut down to the correct size based on the Reseq error profiles. I have now changed this to 500 to allow for profiles with longer reads.)

Hope that helps, Georgette

ajw2329 commented 1 year ago

Fantastic thanks very much!!