Entering edit mode
2.2 years ago
pooryamb
•
0
Dear all,
I am trying to align my reads against a 20nt fragment. Even though I see many reads contain the fragment, bowtie2 cannot align the reads against the target. And it says among the reads, (100.00%) aligned 0 times.
What should I do to align the reads against the target sequence?
The sequence is too short for bowtie2, use the bowtie1 aligner.
It seems odd. It didn't work again. Is there any alternative for aligning against short DNA fragments? I had heard bowtie is more efficient than bowtie2 for very short reads. In my case, my target is 20nt, and my reads are 200nt. Is it supposed to work better than bowtie2 for my case too?
oh my mistake I thought your reads are 20bp
I don't know of any short read aligner that would align against 20bp reference, and especially not a 200bp read
your usecase is completely opposite to what short read aligners are used for - a short read aligner should not be thought of as an optimal aligner that will find the best alignment no matter what - rather think of them are quick methods to find alignments that are close to perfect while ignoring everything else
maybe something like bbduk.sh can be used to find out which reads have the 20nt fragments