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sanjaynagi / AmpSeeker

A snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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set standards for bed file, and accompanying tsv file #8

Closed sanjaynagi closed 1 year ago

sanjaynagi commented 2 years ago

What columns are required?

sanjaynagi commented 2 years ago

Instead of current 'AgamDaoInfo.tsv' file - Should we just use a bed? with extra columns for metadata?

sanjaynagi commented 2 years ago

and for metadata, what columns should we need?

make example files.

sanjaynagi commented 1 year ago

bed file - chromosome / start / stop / name (aa_change) / gene

metadata - sampleID / cohort / species / latitude / longitude

sanjaynagi commented 1 year ago

We now require

bed file - chromosome / start / stop / name (could be aa_change) / type metadata - sampleID / taxon / country / location / latitude / longitude

sanjaynagi commented 1 year ago

Closing for now

ChabbyTMD commented 1 year ago

Hi Sanjay, could you please send me the AgamDao.bed file you used in the config directory.

sanjaynagi commented 1 year ago

Hey Trevor. I can’t send you it as I’m on vacation now until next Tuesday. But the bed file has 5 columns with no header - chrom, start, stop, snp_name, snp_type.Currently snp name and type are not being used but will need to be present SanjSent from my iPhoneOn 18 May 2023, at 08:13, Trevor Mugoya @.***> wrote: Hi Sanjay, could you please send me the AgamDao.bed file you used in the config directory.

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