Comments (5)
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?
from fastq-screen.
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
from fastq-screen.
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
from fastq-screen.
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
from fastq-screen.
This is done and will be included in the next upcoming release.
from fastq-screen.
Related Issues (20)
- R1 and R2 generate map differently to the human genome HOT 4
- Error with certificate for --get-genome HOT 7
- Error while performing --bisulfite read mapping HOT 4
- --get_genomes download failed HOT 8
- Support for STAR HOT 2
- Fail to install GD module HOT 1
- can we download a subset of index database? HOT 1
- Only "no hits" in the output!! HOT 3
- Question- how to include no hit reads into final fastq data while screening? HOT 1
- Using pigz for parallel gzip operations HOT 2
- FastQC on output HOT 5
- Skipping DATABASE HOT 1
- issue installing.. HOT 1
- Filtering bisulfite fastq files HOT 3
- Unable to download v0.15.3 FastQ-Screen or --get_genomes HOT 1
- Filtering was killed HOT 1
- Doesn't match if U nucleotide used in sequence HOT 3
- Reference genomes on Babraham Bioinformatics website are no longer available for download HOT 3
- No reference genomes were configured, please adjust configuration HOT 4
- Question on reads mapping to multiple genomes HOT 1
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from fastq-screen.