Are my .bam files ok?

Question

[jomagrax]

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.

[GenoMax]

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

[cpad0112]

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

Answer 1

[ATpoint]

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.

[jomagrax]

Ok that worked thankyou very much!