denovo assembly of RNA-Seq data obtained from different platform.

Question

[1234anjalianjali1234]

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

Answer 1

[Istvan Albert]

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:

• De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
• https://academic.oup.com/gigascience/article/8/5/giz039/5488105

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

Answer 2

[1234anjalianjali1234]

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?