The input files' structure

[MusculusMus]

Hi,

I am interested in using this workflow to analyze my eCLIP data and have yet to gain experience in eCLIP data analysis.

Your test data contains 8 input files; I assume those include two replicates and two SMI controls. What's the link between these eight files?

From standard paired-end RNAseq of eCLIP, I will get four fastq files from 1 sample: sample1_data1 & sample1_data2 (with SMI1_data1 & SMI1_data2), then from here, how can I have the mate1_3p and mate1_5p files?

Thanks for your time.

Shuai

[mkatsanto]

Hi Shuai,
Indeed these are the two replicates and two SMI controls as you say. The mate1_3p is the 3 prime adapter that needs to be trimmed from mate1 and mate1_5p is the 5 prime adapter. There are also options for mate2_3p and mate2_5p if you look at the config.yaml. These rely on the sequencing protocol used as they do not have the same sequences always and this is why we leave it up to the user.

[MusculusMus]

Thanks for your answer, I should open the fastq file and have a look. No problems with the input files now.

I am reading the readme file which says "Singularity container" only o Linux systems, is it possible to install it on a Windows workstation?

[mkatsanto]

The workflow has not been tested on Windows and to my knowledge Singularity with Windows does not work very well but maybe it is possible. If we test this at any point I will update here.