Stacks2: tvs2bam Single end option not available

[angellcarrasquillo]

Hello, I am trying to run the Stacks2 pipeline on single end data. I had no issues until I reached tvs2bam where I got an error. This error seems to be caused by the "Short read data from individuals" option. I have the options of paired and reversed data. However, as I am using single end data neither of these options are necessary for me. In fact underneath it says "Leave selection empty if you analyse single end data." However, I am unable to leave this section blank and am forced to pick an option, or it defaults to reverse reads. I don't know if this is a design error or a mistake on my behalf, as I have been able to run deNovo before.

Thank you,

Angel Carrasquillo

[bernt-matthias]

Can you tell me which tool version you are using?

[angellcarrasquillo]

I am using version 2.55+galaxy1

On Fri, Dec 3, 2021 at 3:12 AM M Bernt @.***> wrote:

Can you tell me which tool version you are using?

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[bernt-matthias]

@angellcarrasquillo do you have a screenshot of the error? or can you share a history? I can not reproduce this.

[angellcarrasquillo]

It is not necessarily an error, more of a UI issue, the instructions state to leave the selection empty, however, by default it selects an option, and there is no way to leave it blank. When I try to run it with "reverse reads" I have the following error:

Error: Unrecognized paired-end read name format, at 'SRR11700453.2497148 7_2312_6697_25318_1 length=45'. Aborted.

[image: Capture2.PNG][image: Capture.PNG]

On Fri, Dec 3, 2021 at 11:40 AM M Bernt @.***> wrote:

@angellcarrasquillo https://github.com/angellcarrasquillo do you have a screenshot of the error? or can you share a history? I can not reproduce this.

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[bernt-matthias]

Your screenshot did not make it to github. Maybe you can add it directly to the issue?

For me it looks like this:

so even though I have fastq files in my history they are not selected by default. And if I leave them unselected the tool runs as expected.

[angellcarrasquillo]

I am hoping these go through, but the issue is that I am using single end data, and when I try to change the option for "Short read data from individuals. " to empty as instructed, but am unable to do so.

[bernt-matthias]

I see. The Leave selection empty if you analyse single end data. refers to the selection of the data sets below (in the Reads input).

So you can just leave reverse reads selected and do not select any fastq datasets in Reads input.

To improve the UI I see two options:

1. reformulate the help there
2. add a third option single ended data which won't show any fastq selection input parameter.

Which would you prefer?

[angellcarrasquillo]

I see, to improve UI I would suggest adding a third single ended data option which won't show fastq selection.

Thank you for your help

On Fri, Dec 3, 2021 at 1:52 PM M Bernt @.***> wrote:

I see. The Leave selection empty if you analyse single end data. refers to the selection of the data sets below (in the Reads input).

So you can just leave reverse reads selected and do not select any fastq datasets in Reads input.

To improve the UI I see two options:

1. reformulate the help there
2. add a third option single ended data which won't show any fastq selection input parameter.

Which would you prefer?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/galaxyproject/tools-iuc/issues/4269#issuecomment-985751353, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWYCXKSVKPMZTAZ2PCUMZODUPEGYDANCNFSM5JHPQGCA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.