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Question: BAM files on IGV look empty
0
gravatar for EHC
14 months ago by
EHC • 10
EHC • 10 wrote:

Thanks for your previous help. I use these demonstration files https://zenodo.org/record/582600#.WczAmkojFhA uploaded them as fastqsanger and run bwa-mem with NC_007795.1 reference after NormalizeFasta. I got a BAM file.

I would like to view the BAM on IGV locally but can not. I have igv locally and open it first then click the link for "display with IGV local" but files appear empty even if I zoom to 100bp. I also download the galaxy bam/bam.bai files from Galaxy and upload to igv independently. it also seems empty.

I would appreciate your help. thanks!
bwa-mem igv bam • 671 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by EHC • 10

How big was the file when you downloaded it?

ADD REPLY • link written 14 months ago by Devon Ryan • 1.9k

bam 3.1MB; bam.bai 2 KB Thanks!

ADD REPLY • link written 14 months ago by EHC • 10
0
gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Closing this out under the assumption that this is now working. Please let us know if you need more help.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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