Dear all,
I was wondering if anyone has ever tried filtering (potential) small RNA from a regular RNAseq transcriptome .
I have 38 assembled transcriptomes of a particular organism in different circumstances. I was thinking that these should contain small RNA as well, and that I could filter them out, based on transcript size, but that it might be difficult to make the difference between degraded regular RNA and real small RNA. The upside is that I also have a well-assembled genome of the organism in question, so I figure I could align the transcripts with the genome and remove most of the degraded transcripts this way.
Has anyone ever tried this and if so, with success or not?
Eager to use all the info in my data, but still wanting to use the time wisely!
Cheers,
Stephanie
I was wondering if anyone has ever tried filtering (potential) small RNA from a regular RNAseq transcriptome .
I have 38 assembled transcriptomes of a particular organism in different circumstances. I was thinking that these should contain small RNA as well, and that I could filter them out, based on transcript size, but that it might be difficult to make the difference between degraded regular RNA and real small RNA. The upside is that I also have a well-assembled genome of the organism in question, so I figure I could align the transcripts with the genome and remove most of the degraded transcripts this way.
Has anyone ever tried this and if so, with success or not?
Eager to use all the info in my data, but still wanting to use the time wisely!
Cheers,
Stephanie
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