Problems loading fragments file

[A-legac45]

I am Anne-laure Le Gac woriking on the EPIMAIT project from olivier teams. I have a problem when I want to load my fragments.tsv.gz file

warning : can't find any specified file types in the upload folder

Do you know how to manage this problem?

[Pacomito]

Hello Anne-Laure,

This might be because your folder is not organised in a way that ChromSCape can recognise or that you mis-selected the base directory.

I will show an example with images:

1. Here is an example of organised folder for fragment files (this is the same for Sparse Matrix & Single-Cell BED inputs):

Note that each sample is placed in its own folder (e.g. GBM_H3K27me3) containing the fragment file and it's index (optional). All the folders are placed in the same directory (e.g. Fragments/), which is the directory you have to select in ChromSCape.

2. In ChromSCape, tick the 'Fragment File' input data type and click on the button 'Select folder containing raw files'

3. Then select the base directory 'Fragments' and click on 'Select'

4. Finally, remove the unwanted samples by clicking in the 'Selected samples' area and removing samples with the backspace key, and click on 'Create Analysis'