Are my .bam files ok?
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18 months ago
jomagrax ▴ 30

Hi everyone my name is Jos, this is my problem:

I have downloded some .bam files compressed in .rar, I decompressed them with both winrar and the command unrar obtaining this:

file control_1.bam control_1.bam: gzip compressed data, extra field

when I try to see the file this message comes up

head control_1.bam head: error writing 'standard output': Input/output error

What that means, thankyou in advance.

alignment • 605 views
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BAM files are binary so you will not be able to see anything with head.

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Instead of head, try using dedicated tools such as samtools, seqkit or picardtools to read bam file.

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18 months ago
ATpoint 52k

Use samtools quickcheck to check file integrity. Details can be found in the samtools documentation.

head on bam makes no sense as it is binary, instead do samtools view your.file | head

Make yourself familiar with samtools as it is a key application to work with SAM/BAM format.

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Ok that worked thankyou very much!

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