Adaptor and input fastq files

[MusculusMus]

I came across this workflow, and it's perfect for me, who has little experience with command line scripts. I have the same question with Adaptor issue.

1. Should I just leave the default setting there? Will the pipeline detect and remove the standard Illumina adaptor? adapters: dna: randomer_size: 10 rna: name: X1A sequence: AUAUAGGNNNNNAGAUCGGAAGAGCGUCGUGUAG
2. The code specifies the input location in the same config.yaml. Where should I create the reads folder?
3. Does this workflow accept paired-end sequencing data? Should I merge paired-end sequencing fastq files as one?
4. Are the ip1 and input1 from same sample?

[NanoCoreUSA]

Hi @MusculusMus,

So sorry for the late reply, I switched GitHub accounts after moving to a new institution and wasn't receiving the notifications.

To answer your questions -

1. The adapter specified in the config file should be the RNA used in the library prep. We typically use the X1A/X1B adapters, but it can be any of the other adapters that are outlined in the original eCLIP paper. The Illumina adapter is hard coded into the pipeline and will be removed automatically.

2. The 'reads' folder should be created within the working directory (the folder that's created after cloning the meCLIP repo (see the 'Prepare Working Directory' in the README for more details).

3. Yes, the workflow is specifically designed for paired-end sequencing and doesn't work with single-end. You must specify the forward and reverse reads in the config file for both IP and INPUT samples.

4. No, 'ip1' is the forward read of the IP sample, and 'input1' is the forward read of the input sample. The IP sample is the one treated with the anti-IP antibody, and the INPUT is the sample obtained prior to treatment with the antibody (see our meCLIP paper cited at the bottom of the paper for a complete description of the library prep).

Hope that's helpful, feel free to reach out if you have any more issues.