Hello all,
I am trying to use Bowtie to align paired end sequencing data from solexa, but I am consistently getting
I have tried running Bowtie's single end mapping, and have gotten both ends to align with >90% of the reads with at least one reported alignment, but the second I try paired-end, the whole thing fails, and there are no error messages to give me some sort of hint as to what is happening.
is the command that I am using. Has anyone else run into this problem before? Does anyone have any ideas as to what I should do to get some of the reads to align properly?
-Rahul Dhodapkar
I am trying to use Bowtie to align paired end sequencing data from solexa, but I am consistently getting
Code:
# reads processed: 3188 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 3188 (100.00%)
Code:
./bowtie -S -t -p 8 -q --chunkmbs 128 hg18_combined.fa.bowtie -1 Pair1.fastq -2 Pair2.fastq bowpeout.sam
-Rahul Dhodapkar
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