problem with bowtie????

Anonymous
2012-04-26
2013-06-05

  • Anonymous
    2012-04-26

    Hi:
    I have run into couple problems with bowtie recently, could anyone give me a hint of what happened??  Thanks

    Problem one:
    I try to run a bowtie match with around 5754000 sequence read in fasta formate using bowtie.
    The comment line was
    ./bowtie -f -v 0 -S
    but this is the output I got, only ~ 1/80 reads get processed

    # reads processed: 85642
    # reads with at least one reported alignment: 59065 (68.97%)
    # reads that failed to align: 26577 (31.03%)
    Reported 59065 alignments to 1 output stream(s)

    I have used bowtie many times, and it only have problem with this particular sample,

    Problem two:
    I tried to look for a group of reads without T at the end, but after I ran bowtie, I found there is a small portion of reads have T in the output file.
    Is this an expected outcome?

    Thanks