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implementing the pipeline for single tumor sample per patient #9

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ShahiRB opened this issue Oct 2, 2020 · 2 comments
Open

implementing the pipeline for single tumor sample per patient #9

ShahiRB opened this issue Oct 2, 2020 · 2 comments

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@ShahiRB
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ShahiRB commented Oct 2, 2020

Hi Claire,

When I go through the "run_kma_example.R" script provided, it looks like the pipeline is only designed for cohort/multiple samples/multiple conditions analysis. But are there ways to implement the pipeline for single tumour sample per patient?
And, I wonder from where "decoder_all.txt" file came from and what is the content of this file? Does it contain the input file structure mentioned in kma? i.e;

experiment
|____conditionA
| |____conditionA1
| |____conditionA2
| |____conditionA3
|____conditionB
| |____conditionB1
| |____conditionB2
| |____conditionB3

Regards,
Rajendra

@ptnaimelmm
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Hi Rajendra,

Have you worked this pipeline successfully? I got some problems using this pipeline.

@ShahiRB
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ShahiRB commented Apr 12, 2022

No :(

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