Question: Finding Novel Transcripts From A De Novo Transcriptome Assembly
1
gravatar for ilovepython
7.3 years ago by
ilovepython130
ilovepython130 wrote:

I've assembled a de novo transcriptome from RNAseq data. I'm comparing it against a reference cDNA set that is publicly available. However, I'd like to see if my assembly has produced any novel transcripts. Is there something like a reverse alignment? I'd like to find transcripts that I've assembled that are not included in this file of cDNA. I will then map them to the genome using blat or a similar tool.

How can I do what seems like the inverse of an alignment?

assembly denovo transcriptome • 2.1k views
ADD COMMENTlink written 7.3 years ago by ilovepython130
2
gravatar for Nicolas Rosewick
7.3 years ago by
Belgium, Brussels
Nicolas Rosewick7.9k wrote:

Check here : http://biostar.stackexchange.com/questions/14908/extract-unmapped-reads-from-blast

ADD COMMENTlink written 7.3 years ago by Nicolas Rosewick7.9k
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