Question: denovo assembly of RNA-Seq data obtained from different platform.
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gravatar for 1234anjalianjali1234
22 days ago by
India
1234anjalianjali123430 wrote:

hello,

I am trying to merge the different RNA-Seq raw data available on NCBI-SRA corresponding to different studies to make a denovo-assembly. But the data are from different platforms viz. Illumina Hiseq 2000,2500,4000, Illumina GAIIxand and LS454, some of which are SE while others are PE. I want to make combined assembly using these samples and then removing batch-effect for differential gene expression analysis.

I am not able to find any tool for this type of analysis. Need help...

Thankyou

ADD COMMENTlink modified 21 days ago • written 22 days ago by 1234anjalianjali123430
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gravatar for Istvan Albert
21 days ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

Batch effect has a different meaning for transcriptome assembly, and, seemingly counterintuitively, you may want to combine data with batch effects.

For example, different tissues, cells subjected to different conditions may express different transcripts. It would be advisable to assemble your transcriptome using all these potentially varied data, to be able to identify as many isoforms as possible. Many tools allow combining different types of reads. Here is an overview:

Now, the batch effect removal for differential expression quantification is a completely different task, unrelated to the transcriptome assembly.

ADD COMMENTlink modified 21 days ago • written 21 days ago by Istvan Albert ♦♦ 86k
0
gravatar for 1234anjalianjali1234
21 days ago by
India
1234anjalianjali123430 wrote:

Thankyou for your help,

I have gone through various assemblers of which i have found that Velvet and SoapdenovoTrans could do assembly for both SE and PE reads but the main problem is that velvet is a genome assembler, i am not sure about trinity doing the same thing? any help regarding velvet and trinity for the combined assembly?

ADD COMMENTlink written 21 days ago by 1234anjalianjali123430
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