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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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Read minimum length & small RNA mapping #156

Open vibsd opened 1 year ago

vibsd commented 1 year ago

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 commented 1 year ago

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

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 GitHubhttps://github.com/wwood/CoverM/issues/156, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAADX5D53HML6RBNMITSJBDWVIPZTANCNFSM6AAAAAAUNN3PDM. You are receiving this because you are subscribed to this thread.Message ID: @.***>

vibsd commented 1 year ago

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 commented 1 year ago

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