Snap aligner to Igv?
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:
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:
The files I used are working in Bowtie for example, so they cannot be the problem. What am I missing here?
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Just to confirm. You first sorted and then indexed BAM files, correct?
Yes. I followed the exact same routine as with Bowtie.
do you see any read with
samtools viewin the region you're looking with IGV ?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.
I don't understand your answer, but try to write the correct contig name in IGV....
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.
Why would SNAP change your contig names? Did it do that during the index creation?