igv beginer question
1 answer
I guess you are puzzled by too many mismatches between reads and reference. Check that the version of the genome in IGV is the same as the version you used for alignment (e.g. both are hg38 as opposed to one being hg37 and the other hg38). Another possibility is that the index of the alignment file is corrupted. If so, just recreate the index with samtools index.
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Probably a bit off-topic, but if you're interested in learning more about IGV, you might find this recently published Udemy course useful: https://www.udemy.com/course/reading-structural-variants-in-igv-short-read-ngs/?referralCode=329A93865E96ACB13973
It focuses on the practical interpretation of CNVs and structural variants in short-read NGS data, with an emphasis on understanding what the patterns seen in IGV mean in a clinical context.
There's also a concise illustrated guide on Gumroad for quick reference: https://larkass.gumroad.com/l/qvvczb
Yes, off-topic. You announced your course already in a Tutorial post. Leave it at this, please. No need to revive a lot of old IGV posts.