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anchor seed

Can anyone explain What is the anchors and alignment window in the STAR aligner algorithm?

Thanks

rnaseq staraligner
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updated by Ram Ram • written by archanaverma433 • archanaverma433

Did you read the manual? What does it say about these factors and do you have any specific questions from that text?

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written by Ram Ram

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.

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written by archanaverma433 • archanaverma433

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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written by Ram Ram

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