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Compatability with recentrifuge? (add read len to the output) #198

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rjsorr opened this issue Feb 22, 2022 · 4 comments
Open

Compatability with recentrifuge? (add read len to the output) #198

rjsorr opened this issue Feb 22, 2022 · 4 comments
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enhancement New feature or request

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@rjsorr
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rjsorr commented Feb 22, 2022

Hi
I'm wondering as to the compatability of ganon (classify/report) output with recentrifuge (https://github.com/khyox/recentrifuge/wiki/Running-recentrifuge-for-a-generic-classifier)? I need to remove contaminant reads from the dataset and for a person who doesn't use R (Decontam), then recentrifuge seems like the best option. As such, I'm wondering if a) the ganon output is compatible with Recentrifuge (which I presume it is)? and b) What output, either from classify or report, will give me a file that is closest to the requested input of Recentrifuge?
@pirovc
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pirovc commented Feb 23, 2022

The file that would be the closest is either the lca (--output-lca) or complete output (--output-all). Those files report 3 fields: read id, target (taxid), k-mer/minimizer count.

You could use the k-mer/minimizer count as the score for recentrifuge but the read length is not reported, you'd have to add to those files after the run.

@rjsorr
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rjsorr commented Feb 23, 2022

Cheers @pirovc !
I'll add/match the read length column and give it a try

@khyox khyox mentioned this issue Feb 23, 2022
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@pirovc pirovc added the enhancement New feature or request label Mar 16, 2022
@pirovc
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pirovc commented Mar 16, 2022

@rjsorr any success running recentrifuge with ganon? I'll leave this open as a possible enhancement

@pirovc pirovc changed the title Compatability with recentrifuge? Compatability with recentrifuge? (add read len to the output) Mar 16, 2022
@rjsorr
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rjsorr commented Mar 22, 2022

see for compatability solution: khyox/recentrifuge#35

@pirovc pirovc closed this as completed Mar 23, 2022
@pirovc pirovc reopened this Mar 23, 2022
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@pirovc @rjsorr