Snap aligner to Igv?

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4.1 years ago

newbie • 0

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: Igv

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

snap igv aligner • 1.2k views

ADD COMMENT • link 4.1 years ago by newbie • 0

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

ADD REPLY • link 4.1 years ago by GenoMax 141k

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

ADD REPLY • link 4.1 years ago by newbie • 0

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

ADD REPLY • link 4.1 years ago by Pierre Lindenbaum 161k

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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 REPLY • link 4.1 years ago by newbie • 0

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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 REPLY • link 4.1 years ago by Pierre Lindenbaum 161k

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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 REPLY • link 4.1 years ago by newbie • 0

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

ADD REPLY • link 4.1 years ago by GenoMax 141k

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