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mapDamage error

Hi everyone, I am a molecular biology student, new to bioinformatics and I need some help.

I have downloaded the .bam files from the 1000 genomes project (high coverage phase 3), I would like to simulate damage using MapDemage but the programme seems to give me an error. I used the command line

mapDamage -i input.bam -r reference.fasta -d mapdamage_output

As an output file it only downloads the Runtime_log.txt and I don't understand why.

Also when I run the command it seems to give me problems with the reference sequence (you can see it in the screenshot). I am using a hg18 reference sequence.

Do you know how to solve this problem?

enter image description here

Thank you all very much

mapdamage 1000genomes
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written by anna.utili • anna.utili

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

I don' know your software, it looks like you have a problem with the mitochontal genome in your reference sequence. Somewhere the mito genome is called MT (size = 16569) and somewhere else it's called M (size = 16571). Check the reference/fasta vs your data: the fasta you're using is not the one that was used to map the bam.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you very much for your reply and advice! Unfortunately I cannot find the fasta reference used for phase 3 genomes

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written by anna.utili • anna.utili

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