Batch CRISPRessoPooled

[jsacco1]

I really appreciate the Batch function, but I would like to have a feature for multiple (batch) of CRISPRessoPooled samples.

I have to currently make a custom script to make separate txt files for each CRISPRessoPooled sample (which itself corresponds to 2 fastq files). Then run each sample individually:

CRISPRessoPooled -r1 fastq_R1.fastq.gz -r2 fastq_R1.fastq.gz -f sample_name.txt

It would be great if there could be a function that mimicked Batch, because sometimes I have experiments with ~10 samples. Something like:

CRISPRessoPooled -bs input.txt

Just a function where I don't have to keep manually inputting r1 and r2. Is there a quick workaround for this?

Thanks

[kclem]

HI @jsacco1 Thanks for using CRISPResso!

Would the function fo this program just be to read the CRISPRessoPooled parameters in from a file, and then to run them all? Or are you hoping that it would also aggregate the results after the run and produce an html file with links to the results?

If you're hoping to aggregate, do each of your pooled runs necessarily have the same amplicons? Or how would this information be aggregated in the most useful way?