User: shim

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shim10
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Posts by shim

<prev • 7 results • page 1 of 1 • next >
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Comment: C: alignment score and other values for the whole paired-end alignment (with overla
... thanks for your answer and confirming what I suspected. Btw, in my case, at least in bowtie2, MAPQ contributes not much value (many alignments get the same value). ...
written 15 months ago by shim10
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alignment score and other values for the whole paired-end alignment (with overlap)
... Hi, SAM file specification has fields/tags such as alignment score (AS:i: in bowtie2) and edit-distance (NM:i:) for each end of the pair. I am working with amplicons paired-end data (thus overlap is not uncommon) and would like to know if there is a paired-end "combined" score for the whole mate/ ...
bowtie2 paired-end alignment sam scores written 15 months ago by shim10 • updated 15 months ago by Devon Ryan90k
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Comment: C: bowtie2 - Can anybody explain the mismatches in the alignment if no mismatches a
... I've already looked at both bowtie2 manual + paper + supplementary. I might ask the authors ...
written 23 months ago by shim10
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Comment: C: TLEN/Insert size in bowtie2
... thanks (I fixed... your guess was pretty close ;) enough to show the idea) ...
written 23 months ago by shim10
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Comment: C: bowtie2 - Can anybody explain the mismatches in the alignment if no mismatches a
... Thanks for your answer. I do not exactly understand how you EXTEND the alignment. I do assume it is by "merging" the successful adjacent aligned seeds (more efficient than trying to extend every aligned seed). So I guess the only explanation of mismatches in the read (P>0; N==0 is default in bow ...
written 23 months ago by shim10
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how is TLEN calculated in bowtie2
... Hi all, I want to know how TLEN is calculated in bowtie2. Below is the alignment (ran on paired-end) using the CIGAR fields. The alignment is presented as R1,reference, and R2 aligned one below the other (I put R for the NTs of the reads R1, reverse complemented R2, and F for the NTs of the referenc ...
bowtie2 alignment sam tlen bowtie written 23 months ago by shim10 • updated 22 months ago by Biostar ♦♦ 20
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bowtie2 - Can anybody explain the mismatches in the alignment if no mismatches are allowed in the seed?
... Hi, I'm doing an alignment to multiple relatively short targets that are quite similar. I'm using bowtie2 for its local-alignment capabilities (and since I'm used to it). I read the manual + some of the paper + suppl, and am still not quite sure I understand how the alignment procedure works. I ...
bowtie2 alignment seeds bowtie mismatches written 24 months ago by shim10 • updated 23 months ago by Biostar ♦♦ 20

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