Can anyone explain What is the anchors and alignment window in the STAR aligner algorithm?
Did you read the manual? What does it say about these factors and do you have any specific questions from that text?
all the alignments that map less than a user-defined value (typically 20-50) are selected as anchors. this concept I am not getting? Is this MMP? need of anchors. and the anchor region is the genomic window because it says Alignment windows are genomic
regions selected around the anchors.
You may want to email Alex Dobin directly and be as specific as you can. Alternatively, you can wait for others to respond here - it will help if you edit your post and add as much detail as you can. For example, where does it say the "typically 20-50" that you mention? I read the paper, and it mentions picking a subset of seed alignments as anchors, but I cannot reconcile that with what you're saying. Quote your source verbatim (and also link to the source you're quoting) and pinpoint the phrases that you don't understand.
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