Question: Does trinity discard reads shorter than 25-mer?
0
gravatar for lwc628
4.8 years ago by
lwc628210
United States
lwc628210 wrote:

I was curious if Trinity discard reads shorter than its default 25mer. 

The reason why I asked is after quality checking and trimming, there are reads in my fastq files that are shorter than 25. I wanted to know what would happen to them in Trinity.

I assume they(reads shorter than 25 bases) would get discarded as they would not be included in the 25-mer library, but wanted to confirm this

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by lwc628210
3
gravatar for Damian Kao
4.8 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

It would not be used in the Inchworm step as it uses jellyfish to hash the 25-mers. Jellyfish would just skip reads < 25. However maybe it is used in the mapping back steps in chrysalis. I would ask this on the official Trinity mailing list. The developers are usually pretty fast at replying to questions.

ADD COMMENTlink written 4.8 years ago by Damian Kao15k
2
gravatar for lwc628
4.8 years ago by
lwc628210
United States
lwc628210 wrote:

I posted this question in the Trinity user group, and here is what Mr. Haas responded to my question:

###

I'm pretty sure that reads shorter than 25 will simply be ignored. I know they'll be ignored by the kmer counting step (initial part of Trinity), and pretty sure they'll be ignored later on by the Chrysalis/Butterfly stage.  

 

Note, unless your reads are at least ~50 bases in length, for the majority of your reads, Trinity might not be the best application for you.  You can still give it a whirl, though. Definitely try others too, for sake of comparison.

best,

 

~brian

ADD COMMENTlink written 4.8 years ago by lwc628210
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