mapDamage error

Question

[anna.utili]

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?

Thank you all very much

[Pierre Lindenbaum]

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Answer 1

[Pierre Lindenbaum]

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.

[anna.utili]

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