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