Question: BAM files on IGV look empty
0
gravatar for EHC
10 weeks ago by
EHC10
EHC10 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 • 131 views
ADD COMMENTlink modified 1 day ago by Jennifer Hillman Jackson23k • written 10 weeks ago by EHC10

How big was the file when you downloaded it?

ADD REPLYlink written 10 weeks ago by Devon Ryan1.8k

bam 3.1MB; bam.bai 2 KB Thanks!

ADD REPLYlink written 10 weeks ago by EHC10
0
gravatar for Jennifer Hillman Jackson
1 day ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 1 day ago by Jennifer Hillman Jackson23k
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