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biological replicates #27

Open jmbeesley opened 3 years ago

jmbeesley commented 3 years ago

Hello

I was hoping for instructions for the analysis of biological replicates.

Is there an example script for doing this? As far as I can tell, all the provided bash scripts contain "number_of_datasets=1".

So I'm curios how to set up the pipeline to run with number_of_datasets=2? As the individual samples have been run separately in a prior step, is there any need to provide fastq files?

Thanks Jonathan

armenabnousi commented 3 years ago

Hi Jonathan,

You can set the number of datasets to 2. You will need to provide the directories for each replicate later in the file as dataset1, dataset2, etc.

make sure you have these parameters set: (lines 5,6,7,31,32)

feather=1 #start from feather or run only MAPS
maps=1
number_of_datasets=1
...
dataset1="/home/jurici/MAPS/PLAC-Seq_datasets/test_dataset2/feather_output/test_set1_current"
dataset2="/home/jurici/MAPS/PLAC-Seq_datasets/test_dataset2/feather_output/test_set2_current"

These 2 parameters are not used when combining replicates and can be ignored:

fastq_format=".fastq"
fastq_dir="/home/jurici/MAPS/examples/test_set1"