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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?
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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. -
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.Comment
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Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...Yesterday, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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