Question: Short Read Mapping for nt 3 and Above
0
gravatar for xeeoff
22 months ago by
xeeoff0
xeeoff0 wrote:

I am trying to map short reads >=5 nucleotide on a reference genome. The sequences less than 7 are not being mapped with the software's I tried. Is there any mapping tool which can align the sequences with nucleotide 3 and above? I have already used following tools. BWA Bowtie Segemehl Tophat

alignment assembly • 497 views
ADD COMMENTlink written 22 months ago by xeeoff0
3

Can you elaborate on what you are trying to achieve? Reads of that length are very unlikely to be specific.

ADD REPLYlink written 22 months ago by WouterDeCoster42k
1

WouterDeCoster did not made the comment (yet) but you should not use TopHat anymore ;)

more on topic: have you tried blastn-short or such, I'm guessing that any (NGS) read mapper will have trouble (if possible at all) with mapping those very short reads.

Also curious to know how you got such short reads ...

ADD REPLYlink written 22 months ago by lieven.sterck6.7k
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: 695 users visited in the last hour