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#292 bowtie2 only map reverse-complement reference strand

v0.9.0
closed
nobody
5
2013-12-04
2013-10-16
jingyayeah
No

I use bowtie2 map reads back to contigs,the command is ./bowtie2 -f ---end-to-end -x -U -S ,but the result of bedtools coverage reveal the reads mapped only reverse-complement reference strand (-S),but no one to forward reference strand(-s),I think that is anomalous,who can tell the reason and help me?Thanks!

Discussion

  • Ben Langmead
    Ben Langmead
    2013-12-04

    Please supply a specific example where the output of bowtie2 is unexpected. From your description, we can't tell whether this is a problem with bowtie2, your input, bedtools, etc

    Ben

     
  • Ben Langmead
    Ben Langmead
    2013-12-04

    • status: open --> closed