Read minimum length & small RNA mapping

[vibsd]

Dear Ben,

Thanks for this great tool.

I have tried to use it recently to map small RNAs to virus genomes. I was expecting 21 nt long reads to map, indicating that host immune system responded to virus presence. A result I can get with other mapping tools. With CoverM, however, I could see only reads of minimum 30 nt mapping the virus genome.

Is there a minimum read size to use coverM? Can I change this threshold. I looked in the description on github, but could not find the info.

Thanks for your help.

Best,

Vincent

[wwood]

Hi Not sure, never tried. CovrerM won't remove mappings unless you specify filtering parameters which I imagine you haven't. Can you reproduce mappings outside of coverm using minimap2? Do you get no short mappings if you ask coverm to use bwa-mem? -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

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________________________________ From: vibsd ***@***.***> Sent: Wednesday, February 1, 2023 6:51:37 PM To: wwood/CoverM ***@***.***> Cc: Subscribed ***@***.***> Subject: [wwood/CoverM] Read minimum length & small RNA mapping (Issue #156) Dear Ben, Thanks for this great tool. I have tried to use it recently to map small RNAs to virus genomes. I was expecting 21 nt long reads to map, indicating that host immune system responded to virus presence. A result I can get with other mapping tools. With CoverM, however, I could see only reads of minimum 30 nt mapping the virus genome. Is there a minimum read size to use coverM? Can I change this threshold. I looked in the description on github, but could not find the info. Thanks for your help. Best, Vincent ― Reply to this email directly, view it on GitHub<#156>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5D53HML6RBNMITSJBDWVIPZTANCNFSM6AAAAAAUNN3PDM>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[vibsd]

Dear Ben,

thanks for your answer. It turned out that bwa-mem (that I used originally) has length restriction. I could not find how to change it with bwa-mem or minimap2, so I did my analysis differently (using bowtie2 that has no read length restriction).

I am happy to hear if anyone else has another solution.

Cheers,

Vincent

[wwood]

Thanks for the update - perhaps this is an argument for integrating bowtie2 as a mapper..