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Large dataset of RNA-Seq data

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Large dataset of RNA-Seq data

Qihua Liang
Dear MAKER develop team,

I have some RNA-Seq data that I would like to use raw data instead of assembled transcripts in MAKER. But those raw datasets are over 800Gb. I noticed that MAKER will first read all input dataset into /tmp, and my attempts to include such large dataset failed because it exceeds the disk quota. Besides of increasing the disk quota, is there any other option to include such large datasets in MAKER annotations? Or can I redirect MAKER to read those data and use other path to temporarily store those data?

Thank you!
Best
Qihua
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Re: Large dataset of RNA-Seq data

Carson Holt-2
MAKER cannot use raw RNA-Seq. It must be assembled beforehand, or processed into GFF3 using something like Stringtie.

—Carson


> On Apr 6, 2017, at 10:33 AM, Qihua Liang <[hidden email]> wrote:
>
> Dear MAKER develop team,
>
> I have some RNA-Seq data that I would like to use raw data instead of assembled transcripts in MAKER. But those raw datasets are over 800Gb. I noticed that MAKER will first read all input dataset into /tmp, and my attempts to include such large dataset failed because it exceeds the disk quota. Besides of increasing the disk quota, is there any other option to include such large datasets in MAKER annotations? Or can I redirect MAKER to read those data and use other path to temporarily store those data?
>
> Thank you!
> Best
> Qihua
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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