User: verne91
verne91 • 10
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Posts by verne91
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... 10X staff today told me the TLEN is meaningless if the pairs aligned to different chromosomes. ...
written 19 months ago by
verne91 • 10
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Comment:
C: Sorting .bam file by tag
... There is no BX*.sam, because `OUTPUT=substr($0,RSTART+5,18)` ...
written 19 months ago by
verne91 • 10
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... I added the '@PG' tag. So the aligner and parameters are there. ...
written 19 months ago by
verne91 • 10
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... for example:
E00247:267:HMVT3CCXX:2:1208:32603:44398 161 chr1 29691910 25 23M4I37M87S chrUn_gl000220 133398 -307 TTCTCTCTCTGTCTGTCTCTTTCTGCTTCTCTCTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCTTTCTGCTCCTCTCTCTTTCTGTTTGTTTCTCTCCCTGTCGTTCTCCCCCCCCTCCTGTCCCTCTTTCTCTCTCTCTCGCTTCCTTGT AA ...
written 19 months ago by
verne91 • 10
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... How can I calculate the insert size for each entry if I don't use TLEN? just use (rightmost coordinate)-(leftmost coordinate)+1? ...
written 19 months ago by
verne91 • 10
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... I am sorry I made another mistake. I have added the previous example.
Would TLEN be set 0 if the pairs mapped to different chromosomes? ...
written 19 months ago by
verne91 • 10
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... I am very sorry that I took an wrong example. I have updated the example.
I think the problem maybe have something to do with hard clipping. ...
written 19 months ago by
verne91 • 10
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... E00247:267:HMVT3CCXX:4:2219:5172:54541 321 chr1 199910236 45 85H43M chrUn_gl000220 136768 -235 AGAGAGCAAGAAAAAGAAAGAGAGAGAGAGAGAGAGAGAGACA ,7,,,A,,7,A,A,A,A7FAFF,AAF7,, ...
written 19 months ago by
verne91 • 10
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... Why do you subtract the read length in the fourth step? Do the insert size include the read length?
https://www.biostars.org/p/95803/ ...
written 19 months ago by
verne91 • 10
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