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B-UMMI / chewBBACA

BSR-Based Allele Calling Algorithm
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Coding strand convention #193

Closed a-damC closed 8 months ago

a-damC commented 9 months ago

Hello,

I am looking at the cds_coordinates.tsv and results_contigsInfo.tsv output from chewBBACA.

I am unfamiliar with the coding strand convention of 0 & 1 and a google search did not produce any conclusive results.

Is 0 the + (forward) strand or is it the - (reverse) strand?

Thank you, Adam

rfm-targa commented 9 months ago

Hello @a-damC,

chewBBACA <3.3.0 used 1 for the forward strand and 0 for the reverse strand. This has changed for chewBBACA >3.3.0, which uses the strand values assigned by Pyrodigal, 1 for the forward strand and -1 for the reverse strand. We recommend updating chewBBACA if you are not using the latest version. Thank you for opening this issue. We noticed that the docs do not include information about the strand values. We will update the docs soon.

Kind regards,

Rafael

rfm-targa commented 8 months ago

Hello @a-damC,

We updated the documentation pages for the CreateSchema and AlleleCall modules with information about the coding strand convention (included in the description of the cds_coordinates.tsv output file, here and here). I am closing this issue, but let us know if there is anything else.

Kind regards,

Rafael