GSNAP output to IGV

[eperry]

I aligned Illumina reads to the zebrafish v9 reference genome using GSNAP. I had to build a new genome database in GSNAP/GMAP from individual fastA files containing each of the 25 chromosomes. After running GSNAP, I used Samtools to convert the .sam output into a .bam, then sorted the .bam and generated an index file .bai. I want to visualize the alignment using IGV, but I am unsure where to find the correctly-formatted reference file. When I try the fasta files for each chromosome that I used to build the genome database in GSNAP, I receive an error in IGV, saying "sequence.bam does not contain any sequence names which match the current genome". Is the correct genome file found somewhere in the genome database that GSNAP built?

[Brian Bushnell]

I encounter that error a lot. Sometimes it's due to sequences with names containing whitespace, which some programs will truncate and others won't. Look at the header of the sam file and the names in the fasta file and make sure they match.

I recommend that you first concatenate all of the fasta files into a single fasta file, and use that to build an index for mapping, and as input for IGV.

[TiborNagy]

samtools view -h will print the header of your BAM file. Infoseq from emboss or grep "^>" will print out the header of the reference file. You can see how to modify your reference file to fit to your BAM file.