Question: Super Transcripts approach
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gravatar for agata88
10 months ago by
agata88790
Poland
agata88790 wrote:

Hi all!

Have any of you used Corset (https://github.com/Oshlack/Corset/wiki) and Lace programs for contigs to create Super Transcripts? (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1284-1) I found this approach very interesting and wanted to try it on my RNAseq data. From almost 150000 contigs corset and lace programs created 3158 Super Transcripts.

I wanted to run blastx against bacteria database, and I am thinking that it might be wrong... Super Transcripts are long sequences which include few transcripts --> genes. The blast result for such a long sequence will take forever (?). The longest sequence is 284565 bp.

So, my question is, what do you think about running this steps:

  • search for ORFs from Super Transcripts (eg. hmmer2go getorf)
  • then translate it to nucleotide sequences,
  • then align trough blastx and nr bacteria database,

In that way, I will have a nucleotide transcripts (each one representing one gene) and also its aa sequences, ready to go with annotation.

I am curious what are your experiences with Super Transcript approach?

Thanks in advance,

Best, Agata

supertranscripts rnaseq • 344 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by agata88790
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