Bowtie And 100Nt Long Reads

Question

[Gregor Rot]

How does bowtie handle mapping of long reads (in my case 100nt)? Any experience?

Thank you, Gregor

Answer 1

[Fabian Bull]

I mapped 100bp Paired-End RNA-Seq reads using bowtie and Tophat. Everything worked fine.

[Gregor Rot]

Bowtie allows up to 3 mismatches (-v and -n mode), did your 100nt long reads map well anyway? Tnx

[Fabian Bull]

I created an index using bowtie. The mapping was done using tophat. Everything worked well.

[Varun Gupta]

@peri4n Hi can you tell me how you created an index using bowtie. I am just learning about this tool

Thanks in advance RegardS