[maker-devel] Transcript assembly of RNA-seq data from different tissues and individuals

[Fields, Christopher J]

Exactly

chris

From: Carson Holt <carsonhh at gmail.com>
Date: Tuesday, January 31, 2017 at 3:35 PM
To: Quanwei Zhang <qwzhang0601 at gmail.com>
Cc: Chris Fields <cjfields at illinois.edu>, "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Transcript assembly of RNA-seq data from different tissues and individuals

I think he means not to combine them for the transcript assembly preparation (i.e. assembly them separately). But you still provide them all to maker as a comma separated list.

—Carson

On Jan 31, 2017, at 2:33 PM, Quanwei Zhang <qwzhang0601 at gmail.com<mailto:qwzhang0601 at gmail.com>> wrote:

Thank you guys for your suggestions. So you do not suggest to use RNA-seq data from another study, even I assemble them separately and then provide both assemblies into Maker as a comma separated list. The issues you mentioned do exist, but some people did collect RNA-seq data from different individuals and used them for gene annotation (e.g., doi:10.1038/ng.3198). But thank you for your suggestions, I will think about it.
Best
Quanwei

2017-01-31 16:05 GMT-05:00 Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>>:
I agree with Mike.  I also suggest not combining RNA-Seqs from different runs (e.g. different studies) even if they are from the same tissue, development stage etc. There are many other factors (biological variation, sample quality, sequencing chemistry or technology differences, etc) that can significantly and negatively impact trx assembly quality.

chris

On 1/31/17, 1:26 PM, "maker-devel on behalf of Michael Campbell" <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org> on behalf of michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

    I would probably try merging the replicates but not the tissues. You can then pass the output files to MAKER in a comma separated list in the opts file.

    Example:
    est=/PATH/TO/file1.fsata,/PATH/TO/file2.fasta

    Good luck,
    Mike

    > On Jan 31, 2017, at 2:08 PM, Quanwei Zhang <qwzhang0601 at gmail.com<mailto:qwzhang0601 at gmail.com>> wrote:
    >
    > Hello:
    >
    > I am trying to assemble transcripts using RNA-seq data by the tool Trinity, which will be used for gene annotation for Maker. Now I have data from two tissues with two replicates each. Should I merge all four samples to get one assembly file? Or should I merge replicates of each tissue separately and use the two assembly files as input of Maker. Merging all samples into one, we will have much higher coverage level, but I think there may be some genes expressed by tissue-specific isoforms. So I not sure whether I should merge RNA-seq from different tissues.
    > What's more, I find some published RNA-seq data from another individual (and also for different tissue from us) for the same species. Should I merge all RNA-seq together (across individuals and tissues)? Or should I generate different transcript assembly and use all those assemblies as input to Maker?
    >
    > Thanks
    > Best
    > Quanwei
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