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Changing read lengths from the default 150bp #193

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cberta11 opened this issue Jul 21, 2024 · 1 comment
Open

Changing read lengths from the default 150bp #193

cberta11 opened this issue Jul 21, 2024 · 1 comment

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@cberta11
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Good afternoon!
I was wondering if it is possible to change the length of the reads produced using metagenomesimulation.py and wgsim? I am trying to create 300bp paired end reads with a 0% error profile. I bumped the fragment length up to 500bp but am only seeing a read length parameter if suppling my "own" error profile. Thank you so much for any advice! My current config.ini file is as follows:

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@AlphaSquad AlphaSquad added the bug label Jul 29, 2024
@AlphaSquad
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AlphaSquad commented Jul 29, 2024

This is a bit strange, true. It seems to me that this option was lost somewhere and it defaults to 150 now since this is in the constructor. There are a few ways it could be possible to fix this, but for the meantime it might be easiest to change line 70 in the readsimulationwrapper.py file to the read length you require and check if this works.
Since the new nextflow version is almost finished, I don't think this will be fixed for the pre-2.0 versions

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