Could ScreeningProcessing be applied to pair-end sequencing data

[nanu23333]

Hi, thanks for sharing this very useful tool for screening data.

I have a question about the input format:
Can ScreenProcessing be applied to paired-end sequencing data?
Or does it only support single-end FASTQ files (even if the data were generated as paired-end)?

Thanks in advance!

[abearab]

You can check https://github.com/arcInstitute/ScreenPro2 :)

What is the experiment protocol? What do you expect from each of the paired-end sequencing data?

[nanu23333]

You can check https://github.com/arcInstitute/ScreenPro2 :)

What is the experiment protocol? What do you expect from each of the paired-end sequencing data?

Thanks for your reply!

I noticed that the ScreenProcessing tutorial only demonstrates analysis using single-end sequencing data. However, in my experiment, I have paired-end sequencing, and the sgRNA sequence can be present in Read 2.

I would like to ask whether ScreenProcessing can utilize both Read 1 and Read 2 from paired-end data, similar to MAGeCK, or if it is designed to work with only one read (single-end) even when paired-end data are available.