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Discrepancy between table and alignment output #33

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cahuparo opened this issue Sep 24, 2024 · 0 comments
Open

Discrepancy between table and alignment output #33

cahuparo opened this issue Sep 24, 2024 · 0 comments

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@cahuparo
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Hi @zachary-foster,

This is one of the issues we discussed earlier...

> bat default_krisp_outalign.txt | grep -E -B 5 "tccgaatggtagc"
## CM047790.1:12189026-12189132 is diagnostic for ingroup

    Reference: gAtaccacaActccactggcaAttcGcagccttgtacacgcagcatccgaatGgtAgc  G  tacgcagaTggCaacacAcggtcGtaAatgatcatcaaGacgccAttC
 ingroup (64): ..........................................................<G64>................................................
outgroup (16): .R.......R...........R...R..........................K..R..<A16>........Y..Y.....R.....R..R...........S.....R..B
       oligos: gataccacaactccactggcaattc                    tccgaatggtagc  G  tacgcagatggcaa      gtcgtaaatgatcatcaagacgccattc

> bat default_krisp_out.csv | grep -E "tccgaatggtagc"
CM047798.1:12189026-12189132,ingroup,CM047798.1,5,0,12188938,12189156,12189071,12189098,12189026,12189050,12189105,12189132,,cgacggtcgaagattggtcgcatccgtacattgtagtccgacagaagcttgtgaataatcggattgtcgatcgacatttcatcaggtc,gataccacaactccactggcaattc,gcagccttgtacacgcagca,tccgaatggtagcGtacgcagatggcaa,cacacg,gtcgtaaatgatcatcaagacgccattc,gtaggctgacgcttgctagtggct,107,11.045822219368517,gataccacaactccactggcaattc,gaatggcgtcttgatgatcatttacgac,6.61022433014233,4.435597889226187,62.11022433014233,62.93559788922619,48.0,42.857142857142854,0.0,24.646609550538415,0.0,23.32584507586472,0.0,35.822527373322146,2.17,4.34,0.0,0.0

The same region has a different chromosome name in the alignment output.

Thanks,

Camilo

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