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StevenWingett / FastQ-Screen

Detecting contamination in NGS data and multi-species analysis
https://stevenwingett.github.io/FastQ-Screen/
GNU General Public License v3.0
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[Enhancement] Add option to download bisulfite indexes #3

Closed FelixKrueger closed 5 years ago

FelixKrueger commented 5 years ago

If possible, could you please add another option --bisulfite which, when specified in conjunction with --get_genomes, downloads pre-made indexes for Bismark in addition to the Bowtie2 indexes you are already offering.

It might be useful to add to the --help text that this will be in the range of 10-15GB for each normal as well as bisulfite indexes.

Many thanks! Felix redhathero

DiegoZavallo commented 5 years ago

Hi, I was wondering is this enhancement was added. I also want to mapped my reads in --bisulfite mode. Could I just copy the bisulfite index folder into the /Genomes path?

StevenWingett commented 5 years ago

Hi,

This feature will be included in the next update, which should be released in the next day or so. You can of course still use bisulfite genomes that you already have by making sure they are referred to in the configuration file.

All the best,

Steven

DiegoZavallo commented 5 years ago

Thanks Steve, looking forward to the next update. By referred to my bisulfite genomes, do you mean that I have to referred to /path/to/Bisulifte_Genome/ where inside that folder CT_conversion and GA_conversion folders are?

Best

Diego

StevenWingett commented 5 years ago

Hi,

Create a folder called "Bisulfite_Genome" inside the folder that contains the standard Bowtie2 genome index files.

Then copy the relevant "CT_conversion" and "GA_conversion" Bismark folders to the Bisulfite_Genome folder.

Hope that helps,

Steven

StevenWingett commented 5 years ago

This is done and will be included in the next upcoming release.