Truncated chromosomes in IGB

Question

[udi.landau]

Hi,

I have a large genome (600-800 M each chromosome). when I upload the .BAM file into IGB I don`t see any reads align past a certain position (~550 M). I suspect it has something to do with the index file. Does anyone else have this problem? Any suggestions?

Thank`s Udi

[GenoMax]

Tagging: Mason Meyer

Answer 1

[Mason Meyer]

Hello,

My name is Mason Meyer, IGB Support Specialist. I would be happy to help you figure out what you may be experiencing with IGB when loading your BAM file. I am currently looking into the issue to try to reproduce the problem. Is there any way that you could share your BAM file with me so that I could use it for testing this issue?

If you would prefer, please feel free to contact us through the links on our Support Page and we can help figure out why you are experiencing the issue.

Thanks,

Mason Meyer, IGB Support Specialist

[GenoMax]

@Mason a suggestion. You may want to check Biostars once a day if you are the "Support Specialist" for IGB so questions for IGB get answers in a reasonable time. Look for "igb" tags to start identifying posts that pertain to IGB.

[udi.landau]

Hello Mason,

I would like to share with you the bam file if it possible. Maybe with google drive? can you send me your email address?

Thank you

Udi