A question about multimap
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Lanwu Xiao
Nov 17, 2023, 3:24:59 PM11/17/23
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HI Alex,
Thanks for helping with STAR relating problems.
I'm trying to align a read from one single tRNA-Leu (located at chr16) 3'trailer sequence. This read (18 nt) has a mismatch at the 3'-trailer sequence of the tRNA, differing by 1 base from the end. However, I still want to align it to the 3'-trailer sequence of the tRNA. After running the alignment program, I found an identical sequence on chr1, and it is the unique alignment.
So, I set the parameter --outSAMmultNmax 3 to control the number of multiple alignments for the read, and I also set --outFilterMultimapScoreRange +-1 to allow for mismatches. However, the alignment results still show that this read is aligned to the sequence on chr1. How should I set the parameters to align this read to the target tRNA 3'-trailer?
Thanks for helping with STAR relating problems.
I'm trying to align a read from one single tRNA-Leu (located at chr16) 3'trailer sequence. This read (18 nt) has a mismatch at the 3'-trailer sequence of the tRNA, differing by 1 base from the end. However, I still want to align it to the 3'-trailer sequence of the tRNA. After running the alignment program, I found an identical sequence on chr1, and it is the unique alignment.
So, I set the parameter --outSAMmultNmax 3 to control the number of multiple alignments for the read, and I also set --outFilterMultimapScoreRange +-1 to allow for mismatches. However, the alignment results still show that this read is aligned to the sequence on chr1. How should I set the parameters to align this read to the target tRNA 3'-trailer?
Thanks,
Xiao
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