Issue with BAM file from Genome Browser

[Mersedeh]

Hello,

 

I have downloaded a BAM file along with its corresponding BAI file from UCSC Genome Browser DNaseI hypersensitivity from ENCODE. I am trying to open it in IGV and it loads without errors but I don’t see any reads. I read on your website that there maybe a mismatch in chromosome names but I am not sure how to figure that out.

 

Please advise.

 

Thank you,

 

Mersedeh

[James Robinson]

You need to zoom in further, as the messages in the windows indicate,  to see alignments.   By default you need to zoom into a 30kb window,  you can change this window size in the alignment preferences  (User > Preferences > Alignments).

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[Mersedeh Rohanizadegan]

Thank you!

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[James Robinson]

You're welcome.  Most of the Chip datasets are low coverage, so you can probably increase that window size to as much as 1000 kb (1 mb) as opposed to 30 kb.   Experiment until performance suffers.

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