Question: Are my .bam files ok?
0
gravatar for jomagrax
4 days ago by
jomagrax0
Spain
jomagrax0 wrote:

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 • 119 views
ADD COMMENTlink modified 4 days ago by genomax76k • written 4 days ago by jomagrax0
1

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

ADD REPLYlink written 4 days ago by genomax76k
1

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

ADD REPLYlink written 4 days ago by cpad011212k
1
gravatar for ATpoint
4 days ago by
ATpoint28k
Germany
ATpoint28k wrote:

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.

ADD COMMENTlink modified 4 days ago • written 4 days ago by ATpoint28k

Ok that worked thankyou very much!

ADD REPLYlink written 4 days ago by jomagrax0
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