Question: Snap aligner to Igv?
0
gravatar for newbie
5 months ago by
newbie0
newbie0 wrote:

Hi, I try to use Snap aligner (http://snap.cs.berkeley.edu/) and view the result in Igv for some viruses. Here is the Snap output: Snap output

After that, I use samtools to index and sort the .sam file for .bam and .bam.bai. (They are not 0 bytes.) I added the links to Igv (js) and this is what I see: Igv

The files I used are working in Bowtie for example, so they cannot be the problem. What am I missing here?

igv snap aligner • 201 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by newbie0

Just to confirm. You first sorted and then indexed BAM files, correct?

ADD REPLYlink written 5 months ago by genomax89k

Yes. I followed the exact same routine as with Bowtie.

ADD REPLYlink written 5 months ago by newbie0

do you see any read with samtools view in the region you're looking with IGV ?

ADD REPLYlink written 5 months ago by Pierre Lindenbaum130k

Yes, but like this: MN908947.3_Here_is_the_ref_genome_name... This could be the problem? In other bam file which worked fine there is no ref genome name there.

ADD REPLYlink written 5 months ago by newbie0

Yes, but like this: MN908947.3_Here_is_the_ref_genome_name... This could be the problem

I don't understand your answer, but try to write the correct contig name in IGV....

ADD REPLYlink written 5 months ago by Pierre Lindenbaum130k

Snap made my contig like: MN908947.3_Ecoli and in Igv there is MN908947.3 so they dont match. maybe thats why this is Snap beta.

ADD REPLYlink modified 5 months ago • written 5 months ago by newbie0

Why would SNAP change your contig names? Did it do that during the index creation?

ADD REPLYlink written 5 months ago by genomax89k
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