[maker-devel] RNA-seq data for MAKER2

[yuharas at takara-bio.co.jp]

I understand．
Thank you for your useful information.

Satoshi

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 8:37 PM
To: 湯原　悟志; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>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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>
>