Ok that worked thankyou very much!
• 0 views
•
link
written
by
jomagrax •
Are my .bam files ok?
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.
• 3,786 views
•
link
updated
by
GenoMax
•
written
by
jomagrax •
•
written
by
jomagrax •
1 answer
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.
Log in to answer this question.
More posts like this
-
Missing required field on nf-core/sopa
written by jomagrax •
-
CABSdock issue: DSSP call failing
written by charlieclark1ee •
-
Error loading a bam + bai files in IGV
written by jjeang •
-
does salmon support fasta/fastq in tar format?
written by Andrew •
-
Unable to download kraken2 database
written by mathavanbioinfo
-
merge individual runs after bcftools mpileup | bcftools call
written by Leonor •
-
Output file from samtools index is empty
written by dave10808 •
-
Velocyto: Not found cell and umi barcode in entry of the bam file
written by bs58 •
-
samtools index command running slow and truncated EOF warnings
written by vascoambrogi •
-
Miso - no events meet read coverage filter
written by willtun1991 •
BAM files are binary so you will not be able to see anything with
head.Instead of head, try using dedicated tools such as
samtools,seqkitorpicardtoolsto read bam file.