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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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How can I find the "invert_it.pl" wrpper script? #78

Closed Ashar14 closed 3 years ago

Ashar14 commented 6 years ago

I would like to generate the file for the inverted repeats. From the 2013 method puplication, you mentioned the "The wrapper script ‘invert_it.pl’ (Table 2), provided with the Short- Stack tutorial [12], can accomplish all of this."

Bt I could not find the ‘invert_it.pl’ script formt he reference mentioned in abaove publication.

Could you please provide the script.

Thanks

MikeAxtell commented 6 years ago

Hello,

The 2013 paper is quite out of date and the current version of ShortStack does not use input files of inverted repeats. All of the older versions, even super-ancient ones, are on gihub, but I strongly encourage you to use the most recent release.

Thanks, Mike

On Mon, Jul 9, 2018 at 8:51 AM Ashar14 notifications@github.com wrote:

I would like to generate the file for the inverted repeats. From the 2013 method puplication, you mentioned the "The wrapper script ‘invert_it.pl’ (Table 2), provided with the Short- Stack tutorial [12], can accomplish all of this."

Bt I could not find the ‘invert_it.pl’ script formt he reference mentioned in abaove publication.

Could you please provide the script.

Thanks

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-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell

Ashar14 commented 6 years ago

hi, Thank you very much. I will use the recent one. If I understood correctly, you mean that with the new version it is no more necessary to use inv files, right?

MikeAxtell commented 6 years ago

Correct. On Mon, Jul 9, 2018 at 9:00 AM Ashar14 notifications@github.com wrote:

hi, Thank you very much. I will use the recent one. If I understood correctly, you mean that with the new version it is no more necessary to use inv files, right?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell