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Question: Debup Bam ?
0
gravatar for VY
3.7 years ago by
VY • 120
London
VY • 120 wrote:

I Just got back a set of aligned data sets that have been trimmed etc but the files I've received are debup.bam instead of just .bam.

I've uploaded them into galaxy but it doesn't seem to recognize the files or let me work with them as I would usually do with a normal bam file (do peak calling etc).

Any suggestions on how to get around this would be of much help!!

 

thanks :)
bam debup • 1.0k views
ADD COMMENT • link •
modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.7 years ago by VY • 120

Are you sure it is not 'dedup.bam'? That might be deduplicated bam file.

ADD REPLY • link written 3.7 years ago by Martin Čech ♦♦ 4.9k

yes sorry that was a typing error, the file is dedup.bam. I've never worked with this file before so not really sure what it actually is or how to work downstream with it. (Bioinformatics amateur) 

ADD REPLY • link written 3.7 years ago by VY • 120

I would expect it being a standard .bam file, just without duplicates. That said you should wait for someone who knows bioinformatics to respond here. :)

ADD REPLY • link written 3.7 years ago by Martin Čech ♦♦ 4.9k
0
gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This issue is on the public Main Galaxy instance at http://usegalaxy.org? If not, contact the administrator of that other instance if the checks below are OK.

The naming of the files containing the term "dedup" indicates that the SAMTools function by the same name was used to remove duplicates. The format of the BAM file itself should still be in specification. Unless something went wrong upstream or the upload to Galaxy was problematic. Test the data by trying to use it in other applications. Another test is to use SAMtools to convert BAM-to-SAM on the command-line (or any other simple BAM manipulation). 

Best, Jen, Galaxy team
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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