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GenomicsCoreLeuven / GBSX

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments
https://genomicscoreleuven.github.io/GBSX/
GNU General Public License v3.0
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GBSX quality cutoff #1

Closed MBCSD closed 8 years ago

MBCSD commented 9 years ago

Hi,

I'm using GBSX demultiplexer and it works great. Thanks so much for this really nice script. But I'm loosing a lot of samples because their average quality seems to be just a little bit low. It the quality cutoff hardcoded in the script? Is there any way to adjust it?

Thanks so much, Molly

MBCSD commented 8 years ago

Still looking for a way to lower the quality threshold. Anyone have any idea?

Thanks..

KoenHerten commented 8 years ago

Hi Molly,

Sorry for the late answer, but i have been sick for a long time. I did not implement a quality cutoff. This because there are many other scripts that does this. If you think there is, you can always show an example, and I will try to figure out what cause this, for you, unwanted behaviour.

Cheers, Koen

MBCSD commented 8 years ago

HI Koen,

Thanks so much for getting back to me. I’m sorry you’ve been sick. I hope you are feeling better. It looks like we were running into this problem just for that first run. Your script works fine for us now. Thanks so much for making your work available. It’s been very useful.

Best, Molly Dunn

Molly Dunn Crop Genetics

[cid:image002.png@01CE5C41.9EAB9E40]

From: Koen Herten [mailto:notifications@github.com] Sent: Monday, January 11, 2016 5:32 AM To: GenomicsCoreLeuven/GBSX Cc: Molly Dunn Subject: Re: [GBSX] GBSX quality cutoff (#1)

Hi Molly,

Sorry for the late answer, but i have been sick for a long time. I did not implement a quality cutoff. This because there are many other scripts that does this. If you think there is, you can always show an example, and I will try to figure out what cause this, for you, unwanted behaviour.

Cheers, Koen

— Reply to this email directly or view it on GitHubhttps://github.com/GenomicsCoreLeuven/GBSX/issues/1#issuecomment-170502138.

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