[maker-devel] RNA-seq data for MAKER2

[yuharas at takara-bio.co.jp]

Dear Carson

Thank you for your quick reply.
Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
although the tutorial contains information about Tophat and Cufflinks?

Satoshi


-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 11:41 AM
To: 湯原　悟志; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

As far as total depth I don't know, but I'd recommend using something like trinity to assemble the reads and supply them to the est= option in fasta format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for 
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
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