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STAR aligner.. Are reads checked against each chromosome sequentially?

How does STAR, and I guess aligners in general, deal with the order of aligning reads? If reads are first checked against chromosome 1, then 2, and so on, wouldn't that led to a chr1 bias?

star aligners genomics rnaseq
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written by steel1990 • steel1990

Have you looked at the paper to see how the algorithm uses the genome's index when aligning?

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written by swbarnes2 swbarnes2

So the paper doesn't mention 'index' at all, and briefly goes over mapping reads 'contiguously'.. I'm new to bioinformatics, so if you or anyone could explain in simple terms that would be great.

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written by steel1990 • steel1990

I'm new to bioinformatics

All the more reason why it is important that you do your homework and dig into the literature. There are countless resources available that can give you the answers you seek and more.

As an example I found the following which seems like as good starting point as any https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4695832/

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written by jv jv

Correct me if I'm wrong, but one of the useful things about a platform such as this is to ask questions to complicated things, to make things more accessible to someone who doesn't have a sufficient mathematical/computational background? Not answer peoples questions with patronising responses such as 'read more' or 'do homework'... I am assuming you don't know the answer to my question, or are incapable of describing in simple terms as I requested.. In any case, your reply seems to go against the spirit of a collegial platform like biostars

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written by steel1990 • steel1990

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