I am going through the ATAC seq data analysis training and trying to generate a matrix using computeMatrix but it is taking way too long to run - it looks like I am plotting the matrix for the whole human genome.
Can you please have a look at my command liine (please see below) and see if I made a mistake? I did specify, “chr22 genes” as the “Region to plot” but I see “SortBed… ENCFF933NTR.bed.gz” as the “Region to plot” in the tool parameters. Is this where the mistake lies?strong text
Command line:
ln -f -s ‘/data/dnb02/galaxy_db/files/013/749/dataset_13749886.dat’ ‘MACS2 bigwig_0.bw’ && ln -f -s ‘/data/dnb02/galaxy_db/files/013/749/dataset_13749887.dat’ ‘Genrich bigwig_1.bw’ && ln -f -s ‘/data/dnb02/galaxy_db/files/013/750/dataset_13750071.dat’ ‘SortBed on https___www_encodeproject_org_files_ENCFF933NTR___download_ENCFF933NTR_bed_gz_0.bed’ && computeMatrix reference-point --regionsFileName ‘SortBed on https___www_encodeproject_org_files_ENCFF933NTR___download_ENCFF933NTR_bed_gz_0.bed’ --scoreFileName ‘MACS2 bigwig_0.bw’ ‘Genrich bigwig_1.bw’ --outFileName ‘/data/dnb02/galaxy_db/job_working_directory/007/118/7118718/galaxy_dataset_14989742.dat’ --numberOfProcessors “${GALAXY_SLOTS:-4}” --referencePoint TSS --beforeRegionStartLength 1000 --afterRegionStartLength 1000 --sortRegions ‘keep’ --sortUsing ‘mean’ --averageTypeBins ‘mean’ --missingDataAsZero --binSize 50 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id