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

[Quanwei Zhang]

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>:

> 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 on behalf of
> 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>
> 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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