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the proposed pipeline relies on bowtie, which makes mapping of longer reads problematic #8

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yaceya opened this issue May 6, 2021 · 0 comments
Open

the proposed pipeline relies on bowtie, which makes mapping of longer reads problematic #8

yaceya opened this issue May 6, 2021 · 0 comments

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@yaceya
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yaceya commented May 6, 2021

Tried the pipeline with two sided 100b reads and (not completely unexpectedly) got a low mapping rate (around 40%).
The reads mapped 90%+ to the reference genome with tophat2+bowtie2 and 75%+ to the transcriptome.
Any plans to extend the code to run on longer reads? Any workarounds you have tested for now?
Sincerely,
Vasyl
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