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Is there any alternative for CD_Hit to remove redundancy from asemmbled trinity output file?

Hi everyone

I have a problem with reduction of redundancy from trinity output file. I have got an assembled fasta file from trinity containing 302000 contigs showing so much redundancy. I used CD_hit to remove redundancies and get unigenes. After using CD_Hit the number of contigs reduced to 240000 contigs showing lots of redundancies again. CD_Hit was not effective to achieve unigenes. Please give me advise how can I get unigens and remove redundancies?

Thanks

assembly
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updated by bcontreras • bcontreras • written by rahmati.razieh83 • rahmati.razieh83

Did you tweak the identity threshold using -c on the cd-hit?

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written by Sej Modha Sej Modha

When you say

240000 contigs showing lots of redundancies again

How do you verify that?

Try using TGICL

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written by lakhujanivijay lakhujanivijay

3 answers

Trinity has a somewhat new script to construct "SuperTranscripts" based on the gene-to-isoform relationships and the sequence graph structure leveraged by Trinity during assembly. I think this will result in a better representation of unigenes than using cdhit.

$TRINITY_HOME/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py \
   --trinity_fasta Trinity.fasta
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written by h.mon h.mon

Getting 'unigenes' from Trinity assemblies is tricky business. I've found that Corset performs better than CD-Hit. Another idea is to BLAST all the transcripts and group them by reciprocal best blast hit.

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written by Jake Warner Jake Warner

LACE and Corset are tools from the same group. Initially I thought LACE would be the preferred tool, as it was developed more recently, but I was wrong: according to one of the authors of both tools, they should be equivalent for the purpose of doing gene-level differential expression analysis. As the Trinity Trinity_gene_splice_modeler.py is based on the same algorithm as LACE, it should also be equivalent to Corset.

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written by h.mon h.mon

We have used our own https://github.com/eead-csic-compbio/get_homologues successfully. In fact we benchmarked against CD-HIT on https://www.frontiersin.org/articles/10.3389/fpls.2017.00184/full

I believe the main problem is that isoforms with different exons or retained introns are not properly handled by CD-HIT, but can clustered correctly with GET_HOMOLOGUES-EST in most cases

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written by bcontreras • bcontreras

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