How does bowtie handle mapping of long reads (in my case 100nt)? Any experience?
I mapped 100bp Paired-End RNA-Seq reads using bowtie and Tophat. Everything worked fine.
Bowtie allows up to 3 mismatches (-v and -n mode), did your 100nt long reads map well anyway? Tnx
I created an index using bowtie. The mapping was done using tophat. Everything worked well.
can you tell me how you created an index using bowtie.
I am just learning about this tool
Thanks in advance