Closed El-Castor closed 4 years ago
Hi @El-Castor , first you have to convert methimpute output into bedGraph then bedGraph into bigWig, in other words, from menu choice "Convert Methimpute output to bedGraph Format" - item 3 and after that select "Convert bedGraph to BigWig Format" - item 4. Please let me know if you have any questions.
Hi @shahryary ,
Of course I have produce the bedgraph before to produce the bam... but it still some error. My bedgraph is on the good folder and not empty. I have produce big wig from it with my own command, see bellow :
set -e
export PATH="/opt/share/FLOCAD/userspace/cpichot/miniconda3/bin/:$PATH"
# TODO : do optget arg set up for automatisation in Snakemake
### Env loading ###
source activate bedtools
### INPUT ###
bedGraphDir="/NetScratch/cpichot/WGBS_analysis/A2_dominant_andromonoecy_out/bedgraph-format"
chromSizePath="/K/FLOCAD/DATA/OMICS/Melon/DNAseq/AdnaneB/Genome_PacBio/toulouse_assemblage/CMiso1.1/20180606/CMiso1.1_genome.fa.chrom.sizes"
### OUTPUT ###
outDir="/NetScratch/cpichot/WGBS_analysis/A2_dominant_andromonoecy_out/bigwig-format"
mkdir -p $outDir
### OPTION ###
### MAIN ###
for bed in ${bedGraphDir}/*.bedGraph;do
echo "converting bedGraph to bigWig ..."
bedName=$(basename ${bed%.bedGraph})
echo "processing : ${bedName}"
bedGraphToBigWig $bed $chromSizePath ${outDir}/${bedName}.bw
echo "${bedName} convert to bigWig ! "
done
echo "All bedGraph are converted"
This works well, so I think you have some issue on the bedgraph script.
More over I see that the methylkit format file that you produce it contain all the different methylation context but Methylkit is not able to separate the differents context from this file, do do you have any suggestion?
Thanks in advance.
thanks.
Hi @El-Castor
Thank you for the feedback. You right, in Methylkit we are separating based on three contexts (CHH,CHG,CG), and after that running the script to convert into bigwig format, the only thing is coming to my mind after checking the scripts, seems the problem is in the formatting of the file. The point is if you have methimpute output file, you already have context too so it's not going problem during converting BUT missing some column(s) while reading the file( methimpute file) will arise the problem. I suggest, please go through my script to see which columns that I'm importing for converting the file. The script file called "src/bash/meth-bedgraph.R".
Please let me know if you have any questions.
Hi @shahryary,
I'am trying to convert bedgraph to bigwig using your pipeline, but I have an error as you can see below and no production of bigwig a the end:
Do you have any suggestion please ?
Thanks