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Using the given commands for Homo sapiens I am left with 0 rRNAs #3

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biobug16 opened this issue Aug 28, 2019 · 1 comment
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Using the given commands for Homo sapiens I am left with 0 rRNAs #3

biobug16 opened this issue Aug 28, 2019 · 1 comment

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@biobug16
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biobug16 commented Aug 28, 2019 •
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Hi I used the given method to create the ribosomal RNA reference sequence using Rfam 14.1 for humans (species="homo_sapiens"). After following all your steps I am left with 0 rRNAs in order to proceed for quantifying rRNAs in my RNA Seq data set.

I am looking for any solution to my problem.
Thanks
@igordot
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igordot commented Aug 29, 2019

I originally wrote the workflow based on version 12.0, released more than 3 years ago. It should still work for that version. Rfam changed the formatting of their files in the more recent releases.

More recently, I started using RNAcentral, which aggregates data from multiple databases, including Rfam. I updated the workflow to use RNAcentral files.

@igordot igordot closed this as completed Aug 29, 2019
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@igordot @biobug16