Question: denovo analysis of rna seq data
0
gravatar for kartikayprasad
3.5 years ago by
kartikayprasad10 wrote:

Hi all,

I am a master student with biology background. I recently inherit a RNA Seq analysis project from a PhD student in my lab. We already have paired-ended RNA Seq data generated from illumina HiSeq and mapped that sequence using de novo assembly. Now i get contigs but i am now get stuck(i don`t have any reference genome for aligning), now i dont know what to do next.

My aim is to find the novel genes in rna seq data. PLEASE HELP

 

Thanks in advance :)

rna-seq next-gen • 1.2k views
ADD COMMENTlink modified 3.5 years ago by Biogeek350 • written 3.5 years ago by kartikayprasad10
2

Don't you have a supervisor?

ADD REPLYlink written 3.5 years ago by Benn7.5k
1

As you said you are new, so I highly advice to read this review paper it will give you in depth knowledge about what you are doing right now I think it will be so helpful;

ADD REPLYlink modified 11 months ago by RamRS23k • written 3.5 years ago by Medhat8.4k

What software did you use for the de novo transcriptome assembly?

ADD REPLYlink written 3.5 years ago by Biojl1.7k

Right now I am using CLC.

And I am totally new in this.

ADD REPLYlink modified 11 months ago by RamRS23k • written 3.5 years ago by kartikayprasad10
1
gravatar for geek_y
3.5 years ago by
geek_y9.8k
Barcelona
geek_y9.8k wrote:

Basically you have the assembled transcriptome from RNA-Seq data. May be first you need to annotate the transcriptome using some pipeline like trinotate. See few posts below:

Once you have annotated the transcritptome, you can think of different ways to identify novel contigs with coding potential.

P.S I have never done this sort of analysis, so its just my idea.

ADD COMMENTlink modified 11 months ago by RamRS23k • written 3.5 years ago by geek_y9.8k
1
gravatar for Biogeek
3.5 years ago by
Biogeek350
Biogeek350 wrote:

What kind of organism are you working on?

CLCBIO should have an in-software annotation mode. You now should annotate the assembly. You should also check the assembly statistics to see if it is deemed a good assembly. Additionally Have you completed QC on your reads? In order to obtain a good assembly you should remove low quality bases and short sequences.

ADD COMMENTlink written 3.5 years ago by Biogeek350
0
gravatar for akhilvbioinfo
3.5 years ago by
akhilvbioinfo140
India, chennai
akhilvbioinfo140 wrote:

You can use Oases and followed by cap3 to get unigene form your contigs sequence. After that you can annotate unigenes by using various tool like blast or KEGG.

ADD COMMENTlink modified 11 months ago by RamRS23k • written 3.5 years ago by akhilvbioinfo140
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