parallel analysis

[estebanpw]

parallel analysis

[estebanpw]

Hello @Karimi-81

One question, how many fasta files are there for the two genomes?
If there are only two (e.g. genome assembly A and genome assembly B) then you can compare them with the usual command:
./CHROMEISTER -query genomeAssemblyA.fasta -db genomeAssemblyB.fasta -out assemblyAB.mat -dimension 2000 && Rscript compute_score.R assemblyAB.mat 2000

That command will also work for multi fasta files. Now, if there are too many sequences (e.g. thousands and thousands) then you can remove the grid which might otherwise blurr the plot by using compute_score-nogrid.R instead of compute_score.R in the previous command.

Otherwise, if you have LOTS of fasta files there are two options: 1) you can easilty concatenate them using the cat command (e.g. cat *.fasta >> genomeAssemblyX.fasta) or 2) you can use the script you were referring to by running:
allVsAll.sh /chromeister/genomes/ fasta 2000 kmer 32 4 (dont forget the 4 at the end)

That will run an all vs all comparisons and generate a lot of files. Eventually when it completes, it will also generate a csv file including information about each comparison. As to how to run this in parallel, simply re-issue the allVsAll.sh /chromeister/genomes/ fasta 2000 kmer 32 4 (if you are in slurm). The only important thing here is that it must be the same command: the allVsAll.sh script will check if there are files corresponding to the other executions (I know this is a bit of an awkward parallel implementation, but in the future I will make a map approach : -) ).

Important: Lastly, make sure to update your repository, I just pushed an update.

Let me know if this was of help,
Esteban