Full-join/merge the tables from Step 1 (or from Step 2 instead, if applicable). You can provide as many input tables as you want.
mergeBCcounts.R
Please make one collective table for the barcode counts and one for the summaries. Both are needed for the report. That means running this script twice, once for all the barcode count files, and once for all the summary files.
mergeBCcounts.R OUTPUT_FILE INPUT_FILE INPUT_FILE ...
GROUP/Obenauf/catch barcode count merger
The Galaxy implementation of this step merges all the counts tables together and all the summary tables together.
Walltime: Estimated completion time. This step takes a few seconds.
Memory: Estimated memory use. The default 4GB should be plenty. Increase this if you get slurm out-of-memory (oom) / memory-exceeded errors. It will depend on the number of samples and number of identified barcodes.
barcode counts: Select the output from the quantification step. You can also upload samples from other quantification runs as individual table files or as a zipped bundle. NOTE: in order to be recognised, the tables must have filenames that end with _barcode-counts.txt and _summary.txt. If you use outputs from another CaTCH quantification step, this will be already done.