IGVtools 1.5 not showing bam alignments

[ketan_bnf]

Hi

I am using IGV 1.5 to view bam file, but i am not getting tracks in IGV. This is also happening with my vcf file. Why?

I ahve made idex for both the bam/vcf files FYI.

[Yilong Li]

I assume you already tried zooming in closer (IGV does not show reads from very far away), and checking the regions where you know you have coverage, i.e. from locations where the reads are mapped in the .bam file?

[ketan_bnf]

I assume you already tried zooming in closer (IGV does not show reads from very far away), and checking the regions where you know you have coverage, i.e. from locations where the reads are mapped in the .bam file?

NO, i have not zoomed the view. I am by default just giving bam file as input, selecting chromosome sequence to which bam file has alignment record, after that no tracks are shown in the view area.

[honey]

Igv

Rt click expand track and try zooming in

[mapper]

Try running samtools tview command and see if you are able to view alignments...If you can see alignments then there is nothing wrong with your bam files....

I have seen this kind of prob earlier...I relaunched IGV few times and I was able to see alignments...

[ketan_bnf]

Thanks for reply,

i have used tablet to view my bam alignment, can see alignments very well..

For samtools tview i have tried but the problem is it shows 'N' in my chromosome sequece instead of bases when scrolling down the chr,

What is the problem with IGV i don't know, relaunched it many time.

[Yilong Li]

The N's you're seeing are probably the masked telomere of chromosome 1. Trying pressing 'g' in tview and going to a random location like 1:10000000 to see if you can see any ref sequence there.

Also, you need to provide a ref genome to tview ofc.

In IGV, when you open the .bam track, do you see the text 'Zoom in to see alignments'?

Edit: I stumbled upon this in IGV FAQ:

Q: I loaded a BAM file and don't see anything. What's wrong?
The most common cause for this is a mismatch in chromosome names between the BAM file and the IGV genome it is being viewed against. The workaround is to create an alias file in 2-column tab-delimited format. To see how to create this alias file, see Creating a Chromosome Name Alias File in the IGV User Guide.

[ketan_bnf]

The N's you're seeing are probably the masked telomere of chromosome 1. Trying pressing 'g' in tview and going to a random location like 1:10000000 to see if you can see any ref sequence there.

Also, you need to provide a ref genome to tview ofc.

In IGV, when you open the .bam track, do you see the text 'Zoom in to see alignments'?

Yes, i can see 'Zoom in to see alignments' after loading .bam track to IGV

[orf@localhost q20]$ samtools tview GKUNU9Q04_chr1_q20_sort.bam chr1.fa

After applying this command in terminal i can see chr1:1-141 as "AGCTT..." , but when i scroll right to see more base 142-........ , i see "N 's"

Two diff approaches i used,

1) I also tried according to IGV FAQ "chr1.fa <tab> chr1 --> save as org_alias.tab into /home/orf/igv/genome/

2) I added my chromosome to which reads were mapped and .bam (sorted, indexed) file is formed,

but the result is same no tracks shown.

Thanks.

[rururara]

I had this kind of problem too. I only can view my alignment and snps distributions in Artemis and Tablet. Why so hard to view in IGV