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baoe / SEED

Efficient clustering of next generation sequences
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Suggestion to allow 20mers #2

Open MikeAxtell opened 8 years ago

MikeAxtell commented 8 years ago

Hi again, in using SEED to collapse small RNA-seq data from plants, it would be useful if 20 nt reads were allowed as input. There are a few well-known microRNAs that are 20 nts long (for example, miR156). The ideal size range, if the 5nt window of read sizes is key, would be 20-24 nts for most plant small RNA / microRNA data.

Thanks for considering!

baoe commented 8 years ago

Thanks. We will consider extending the seed length values.

Bao

From: Mike Axtell [notifications@github.com] Sent: Friday, June 10, 2016 5:44 AM To: baoe/SEED Subject: [baoe/SEED] Suggestion to allow 20mers (#2)

Hi again, in using SEED to collapse small RNA-seq data from plants, it would be useful if 20 nt reads were allowed as input. There are a few well-known microRNAs that are 20 nts long (for example, miR156). The ideal size range, if the 5nt window of read sizes is key, would be 20-24 nts for most plant small RNA / microRNA data.

Thanks for considering!

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MikeAxtell commented 8 years ago

Thanks

On Fri, Jun 10, 2016 at 11:09 AM, Bao notifications@github.com wrote:

Thanks. We will consider extending the seed length values.

Bao

From: Mike Axtell [notifications@github.com] Sent: Friday, June 10, 2016 5:44 AM To: baoe/SEED Subject: [baoe/SEED] Suggestion to allow 20mers (#2)

Hi again, in using SEED to collapse small RNA-seq data from plants, it would be useful if 20 nt reads were allowed as input. There are a few well-known microRNAs that are 20 nts long (for example, miR156). The ideal size range, if the 5nt window of read sizes is key, would be 20-24 nts for most plant small RNA / microRNA data.

Thanks for considering!

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Michael J. Axtell, Ph.D. Associate Professor Dept. of Biology Penn State University http://sites.psu.edu/axtell Twitter: @MikeAxtell