smoothxg takes gap "-" in the sequence or not

[XuewenWangUGA]

I would like to know whether I can use the equal length of sequences with "-" for the gap as input for pbbg step snoothxg. It seems that the alignment and seqwish in pggb takes "-" but the smoothxg will terminate.
Therefore, is it possible for smoothxg to take gap "-" in the sequence?
Thanks.

[ekg]

I would remove these before seqwish. Can you do that or is it problematic to strip them? We can update the pieces to handle these padding characters. But just because it runs doesn't mean you get a sensible output.

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On Wed, Nov 25, 2020, 20:24 XuewenWangUGA ***@***.***> wrote: I would like to know whether I can use the equal length of sequences with "-" for the gap as input for pbbg step snoothxg. It seems that the alignment and seqwish in pggb takes "-" but the smoothxg will terminate. Therefore, is it possible for smoothxg to take gap "-" in the sequence? Thanks. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#46>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQENLXVSCJC53J5U7DT3SRVKYNANCNFSM4UCZYLIA> .

[XuewenWangUGA]

Erik, Thank you for reply. Look forward to see your update. Happy Thanksgiving. Xuewen

________________________________ From: Erik Garrison <notifications@github.com> Sent: Thursday, November 26, 2020 2:22 AM To: pangenome/smoothxg <smoothxg@noreply.github.com> Cc: Xuewen Wang <xwwang@uga.edu>; Author <author@noreply.github.com> Subject: Re: [pangenome/smoothxg] smoothxg takes gap "-" in the sequence or not (#46) [EXTERNAL SENDER - PROCEED CAUTIOUSLY] I would remove these before seqwish. Can you do that or is it problematic to strip them? We can update the pieces to handle these padding characters. But just because it runs doesn't mean you get a sensible output.

On Wed, Nov 25, 2020, 20:24 XuewenWangUGA ***@***.***> wrote: I would like to know whether I can use the equal length of sequences with "-" for the gap as input for pbbg step snoothxg. It seems that the alignment and seqwish in pggb takes "-" but the smoothxg will terminate. Therefore, is it possible for smoothxg to take gap "-" in the sequence? Thanks. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#46>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQENLXVSCJC53J5U7DT3SRVKYNANCNFSM4UCZYLIA> .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#46 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AGHDDYO35KTLFX2SAKFANFTSRX64XANCNFSM4UCZYLIA>.

[ekg]

To be clear, you should remove them before doing anything, before even mapping. Thanks, cheers :) On Thu, Nov 26, 2020 at 4:56 PM XuewenWangUGA <notifications@github.com> wrote:

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Erik, Thank you for reply. Look forward to see your update. Happy Thanksgiving. Xuewen ________________________________ From: Erik Garrison ***@***.***> Sent: Thursday, November 26, 2020 2:22 AM To: pangenome/smoothxg ***@***.***> Cc: Xuewen Wang ***@***.***>; Author ***@***.***> Subject: Re: [pangenome/smoothxg] smoothxg takes gap "-" in the sequence or not (#46) [EXTERNAL SENDER - PROCEED CAUTIOUSLY] I would remove these before seqwish. Can you do that or is it problematic to strip them? We can update the pieces to handle these padding characters. But just because it runs doesn't mean you get a sensible output. On Wed, Nov 25, 2020, 20:24 XuewenWangUGA ***@***.***> wrote: > I would like to know whether I can use the equal length of sequences with > "-" for the gap as input for pbbg step snoothxg. It seems that the > alignment and seqwish in pggb takes "-" but the smoothxg will terminate. > Therefore, is it possible for smoothxg to take gap "-" in the sequence? > Thanks. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#46>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AABDQENLXVSCJC53J5U7DT3SRVKYNANCNFSM4UCZYLIA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< #46 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AGHDDYO35KTLFX2SAKFANFTSRX64XANCNFSM4UCZYLIA >. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#46 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEMEEDDUFWFKJ5CA6BLSRZ3DDANCNFSM4UCZYLIA> .