Question: single contig de novo assembly
0
gravatar for snishtala03
26 days ago by
snishtala0330
snishtala0330 wrote:

Hello,

I am working with RNA-Seq data for a virus. My collaborator gave me a predicted single contig reference which belongs to a particular genotype (let's say GenotypeA) of the virus. Now, some of my samples are from a different genotype (B,C or D) and therefore their mapping % when aligned to my predicted reference is very low (~24%) when I use STAR.

I think doing a de-novo assembly and then aligning the reads to the new reference should help me. Are there any tools which can do single contig de novo assembly? I tried Trinity but I did not get a single contig from it.

Thanks!

ADD COMMENTlink modified 26 days ago • written 26 days ago by snishtala0330
1

Just a thought: are you certain that all of your RNA-Seq data is pure virus? Have you checked that your other contigs are not something else, e.g. host (depending on how the virus was isolated, obviously)?

I am asking, as I have worked on RNA viruses present in insect transcriptomes. In my case, both Trinity and Velvet/Oases were able to assemble (nearly) full-length viruses among tons of other transcripts (e.g. from the host).

ADD REPLYlink written 26 days ago by cschu1811.9k

Ah, interesting! My host is human. I will try to remove human reads and then try this again.

ADD REPLYlink written 26 days ago by snishtala0330

You can also check the contigs/transcripts that you already have.

ADD REPLYlink written 26 days ago by cschu1811.9k

Appart from the ideas mentiond by @cschu181 I would not necessarily expect a single contig - there migth very well be regions witch are very hard to assemble due to repetitive sequences etc - such regions will cause the assemblies to be broken into many smaller fragments.

ADD REPLYlink written 25 days ago by kristoffer.vittingseerup2.9k
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