Question: problem with bowtie alignment
0
gravatar for Sam
10 days ago by
Sam20
Sam20 wrote:

I have a problem with bowtie alignment, I used bowtie to find match sequence in fastq file with rfam sequence list. I tested it in 2 different conditions: with and without miRNAs sequence in rfam list. But there is a big difference between result in these 2 different condition. When I used complete list of rfam as index , number of match sequence to piRNA is 3,710,548 but after removing miRNAs from rfam list , match seq to piRNA is about 820,000 why I have a big difference in these 2 condition , size of index has influence on alignment ?

Bowtile lunched with this command :

 bowtie /bowtie_index/with-withoutmiRNA_Rfam  in.fq -v 1 --best out.fq

Thanks

bowtie smallrna • 153 views
ADD COMMENTlink modified 10 days ago • written 10 days ago by Sam20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 605 users visited in the last hour