Question: Mapping variable read length
0
gravatar for Chirag Nepal
2.6 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

Hi There,

Does anyone have a recommendation on tools that allow to map reads of variable length (between 18-300 nt) as can be seen here

https://www.dropbox.com/s/10dn098492zst9i/Length.png?dl=0

I had previously (6 years back) used blat to map such cases, and use percent identity to get mapped reads. Are there some new tools that can efficiently map sequence reads of variable length. thanks !!

alignment • 672 views
ADD COMMENTlink modified 4 days ago by Biostar ♦♦ 20 • written 2.6 years ago by Chirag Nepal2.2k
3
gravatar for ATpoint
2.6 years ago by
ATpoint38k
Germany
ATpoint38k wrote:

Any of the popular mapping tools, e.g. bowtie2 or bwa should be able to handle this. What kind of data is this and how certain are you that the small fragments are indeed meaningful and not any noisy byproducts?

ADD COMMENTlink written 2.6 years ago by ATpoint38k
1
gravatar for genomax
2.6 years ago by
genomax89k
United States
genomax89k wrote:

bbmap.sh from BBMap suite should be able to do this.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by genomax89k
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