HISAT2 mapping
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ali • 0
@8da3e03a
Last seen 11 months ago
United States

hi everybody, I have a question about discordant alignment results

23250959 reads; of these: 23250959 (100.00%) were paired; of these: 2462449 (10.59%) aligned concordantly 0 times 19974163 (85.91%) aligned concordantly exactly 1 time

814347 (3.50%) aligned concordantly >1 times
----
2462449 pairs aligned concordantly 0 times; of these:
  1511718 (61.39%) aligned discordantly 1 time
----
950731 pairs aligned 0 times concordantly or discordantly; of these:
  1901462 mates make up the pairs; of these:
    804577 (42.31%) aligned 0 times
    924548 (48.62%) aligned exactly 1 time
    172337 (9.06%) aligned >1 times

98.27% overall alignment rate

approximately, 2462449 pairs aligned concordantly 0 times of these:

  1511718 (61.39%) aligned discordantly 1 time

i cant notice that these results are correct or i have problem in trimming or mapping or....???

actually, i don know , 1511718 (61.39%) aligned discordantly 1 time is a mistake or no??/

thanks for your helping

hisat2 results • 563 views
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ATpoint ★ 3.9k
@atpoint-13662
Last seen 14 hours ago
Germany

hisat2 is not a Bioconductor package. Please ask at biostars.org or elsewhere.

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