.bam track not visible in IGV

Question

[jeffmann131]

Hi folks - you kindly helped me with my related issue of not seeing the gene track in the Ebola IGV visualization in the handbook - this was fixed by converting AF086833.2 to AF086833 in the first line of the fasta file. Now I am having a similar problem with visualizing a BAM file - track seems to go in, but nothing shows. I have zoomed right in to max but still nothing. Also, I have searched the forum and other people report similar issues but not this specific one. Would much appreciate any insights !! Many thanks. I paste in the first lines of the SAM file possibly that may show something that may be causing the issue.

@SQ SN:AF086833 LN:18959
@PG ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa mem AF086833.fa R1_trimmed.fq R2_trimmed.fq
SRR519926.1 77  *   0   0   *   *   0   0   CCGTGAGTAAATTA.....

[jeffmann131]

I think my .bam file is not being produced correctly as it doesn't show in BamView either - will try making it again (indeed for the upteenth time!)

Answer 1

[Devon Ryan]

If that's the first line and the file is sorted/indexed then there are no actual alignments, everything is unmapped...so there's nothing to show.

[jeffmann131]

Devon - thanks for that - I just realised I have been using the wrong SRR number all this time so no wonder there is nothing aligned - thanks again

[Devon Ryan]

Oh no! Well I'm glad you've figured that up now.