Question: BAM files on IGV look empty
0
gravatar for EHC
12 months 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 • 591 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson25k • written 12 months ago by EHC10

How big was the file when you downloaded it?

ADD REPLYlink written 12 months ago by Devon Ryan1.9k

bam 3.1MB; bam.bai 2 KB Thanks!

ADD REPLYlink written 12 months ago by EHC10
0
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson25k 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 10 months ago by Jennifer Hillman Jackson25k
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