De novo small RNA assembly

Juulluu21

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Join Date: Jun 2016

Posts: 6
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#1

De novo small RNA assembly

06-23-2016, 06:52 PM

Hello,

I want to de novo assembly small RNA reads generated from Illumina sequencing (final lengths after clipping and trimming are 18-32nt).

Is there any pipeline available?

I tried Velvet. I used k-mer of 13 to 19 but could not assemble the reads. Assembled reads were maximum 70nt. My library is very deep and outstandingly overlapping (as most are piRNA). I really want to get the whole transcript (assembled).

Is any help out here?

Thanks
-Juulluu21

Last edited by Juulluu21; 06-23-2016, 06:56 PM.
Tags: de novo assemby, illumina & 454, rna-seq, small rna
colindaven

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#2

07-01-2016, 02:34 AM

Sounds tricky - have you tried tadpole - listed on this forum - yet ?
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GenoMax

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#3

07-01-2016, 03:53 AM

Cross-posted and answered by @Brian: https://www.biostars.org/p/198427/
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