discoSnpRAD and short_read_connector

[joannarifkin]

Hi there,

Apparently to run DiscoSnpRAD I need to have short_read_connector installed:

"src_path: absolute path to short_read_connector directory, containing the "short_read_connector.sh" file."

I installed it from https://github.com/GATB/short_read_connector, but there doesn't seem to be a short_read_connector.sh - instead, there are two .sh files, short_read_connector_counter.sh and short_read_connector_linker.sh.

I assume I'm missing something - what should I do?

Thanks and all the best,

Joanna

[pierrepeterlongo]

Hi Joanna

Indeed, wrt recent changes made to short read connector we have to update discoSnpRad. Thanks for pointing this out.
I will propose a correction soon.
In the meanwhile you may use the short read connector commit 4264a626c8d503c55ea34dac5564a786aec368c7

Best,
Pierre

[joannarifkin]

Hi Pierre, Thanks so much - it seems to be working perfectly now. All the best, Joanna

…

On Thu, Oct 1, 2020 at 4:46 PM Pierre Peterlongo ***@***.***> wrote: Hi Joanna Indeed, wrt recent changes made to short read connector we have to update discoSnpRad. Thanks for pointing this out. I will propose a correction soon. In the meanwhile you may use the short read connector commit 4264a626c8d503c55ea34dac5564a786aec368c7 <GATB/short_read_connector@4264a62> Best, Pierre — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPL6CSRGANRN3ZTUTS53RTSITTCHANCNFSM4SAXUYPA> .

-- Joanna Rifkin PhD Department of Ecology and Evolutionary Biology The University of Toronto 25 Willcocks St. Toronto, ON M5S 3B2

[pierrepeterlongo]

Hi again,

I pushed a discoSnpRad version that uses the most recent (1.2.0) version of short read connector. This fixes the problem.

Thanks again,
Pierre

[joannarifkin]

Hi Pierre, Thanks so much. I found plenty of SNPS :) All the best, Joanna

…

On Fri, Oct 2, 2020 at 10:17 AM Pierre Peterlongo ***@***.***> wrote: Hi again, I pushed a discoSnpRad version that uses the most recent (1.2.0) version of short read connector. This fixes the problem. Thanks again, Pierre — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPL6CUEGGO7FDU7MK5QVPLSIXOF5ANCNFSM4SAXUYPA> .

-- Joanna Rifkin PhD Department of Ecology and Evolutionary Biology The University of Toronto 25 Willcocks St. Toronto, ON M5S 3B2