Question: Bowtie And 100Nt Long Reads
1
gravatar for Gregor Rot
8.8 years ago by
Gregor Rot440
Zurich, Switzerland
Gregor Rot440 wrote:

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

Thank you, Gregor

mapping bowtie • 2.1k views
ADD COMMENTlink modified 8.8 years ago by Fabian Bull1.3k • written 8.8 years ago by Gregor Rot440
1
gravatar for Fabian Bull
8.8 years ago by
Fabian Bull1.3k
German
Fabian Bull1.3k wrote:

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

ADD COMMENTlink written 8.8 years ago by Fabian Bull1.3k

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

ADD REPLYlink written 8.8 years ago by Gregor Rot440

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

ADD REPLYlink written 8.8 years ago by Fabian Bull1.3k

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

Thanks in advance RegardS

ADD REPLYlink written 8.6 years ago by Varun Gupta1.1k
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