Question: How to deal with high percentage of non-specific matching during read mapping on Trinity assembly?
gravatar for seta
5.0 years ago by
seta1.3k wrote:

Hi everybody,

Regarding Trinity tool for transcriptome assembly, I noticed that it has high percentage of non-specific matches during mapping reads back to assembled transcriptome. It may almost normal as Trinity generates gene isoforms, too. But, I think it will have an adverse effect on downstream analysis such as gene expression analysis, am I right?. Could you please let me know how you deal with this issue? I also tried reduce redundancy using cd-hit-est tool, but it had not a significant effect on the issue. Looking forward to hearing your solution and experiences.Thanks

ADD COMMENTlink modified 5.0 years ago by h.mon30k • written 5.0 years ago by seta1.3k
gravatar for h.mon
5.0 years ago by
h.mon30k wrote:

Regarding gene expression, Trinity includes Perl scripts to analyze differential gene expression, and the scripts include workflows for "transcript" and/or "gene" levels. The "gene" level analysis is what you want, as it aggregates counts from all isoforms Trinity identified into one "gene".

ADD COMMENTlink written 5.0 years ago by h.mon30k

Thanks. Assuming we want to pool Trinity assembly with another assembly, is there any way to reduce the redundancy before merging assemblies in order to make a non-redundant transcriptome assembly? I used cd-hit-est tool to this end, but I don't know why it was not perfect in this regard, non-specific matching still remained.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by seta1.3k
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