extracting longest unigene from de novo RNA-Seq assemblies

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7.3 years ago

bioming • 0

Helo everyone, After blastx Unigenes.fa from de novo RNA-Seq assemblies to a reference proteome, I obtained the result that multicontigs belong to one gene. So I just try to uniform my data that to remove shorter congtigs and keep the longest contig representing one gene. example is as below:

From origal data

ENSDARP00000143232.1 GGCTCCTCTTTTTCAACTGGACATCCTTAAAACTGTATGAAAGGGGCGGAGCCTTTTGCTACTTGCATACTTAAGCTCCTTCACATTCCTCTAGCCCTTTACGAA ENSDARP00000143232.1 GGCTCCTCTTTTTCAACTGGACATCCTTAAAACTGTATGAAAGGGGCGGAGCCTTTTGCTACTTGCATACTTAAGCTCCTTCAC ENSDARP00000143232.1 GGCTCCTCTTTTTCAACTGGACATCCTTAAAACTGTATGAAAGGGGCGGAGCCTTTTGC

To what I want

ENSDARP00000143232.1 GGCTCCTCTTTTTCAACTGGACATCCTTAAAACTGTATGAAAGGGGCGGAGCCTTTTGCTACTTGCATACTTAAGCTCCTTCACATTCCTCTAGCCCTTTACGAA

Could you give me some suggestions or some scrips to help me, thanks!

RNA-Seq Assembly • 1.2k views

ADD COMMENT • link 7.3 years ago by bioming • 0

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Have u tried cdhit. Use query length to filter from blast file. How did you obtain unigenes?

ADD REPLY • link 7.3 years ago by Prasad ★ 1.6k

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