[scAPP] data/link not working for `JYH_813`

[biomystery]

http://epigenomics.sdsc.edu:8000/setqc/JYH_813/web_summary.html

may be other 10xATAC?

[biomystery]

after merging, JYH_813 no longer shows a correct status.

The summary file is still there:|/home/zhc268/data/outputs/10xATAC/JYH_813/outs/web_summary.html

but in scAPP it is shown clicktosubmit

also http://epigenomics.sdsc.edu:8000/setqc/JYH_813/web_summary.html gives error.

Thanks

[brandonGonzalez01]

Okay, so the problem is that JYH_813 is a scATAC-seq experiment type, the way the code treats it as a scRNA type experiment so it should be in the scRNA_DIR but it is in the TENX_DIR. Do you want scATAC-seq experiments to be stored in the TENX_DIR or the scRNA_DIR?

[biomystery]

can you change the JYH_813 from scATAC to 10xATAC, so that it can be display correctly? You can do it in admin interface.

Also can you check more here: /projects/ps-epigen/outputs/10xATAC? basically make sure all of the libs shown under the folder should be 10xATAC. Let me know if you have any questions. Thanks.

[brandonGonzalez01]

Changed JYH_813 library (pk=1546) to 10xATAC experiment type. results link is now working.

[biomystery]

thanks for fixing this and added all the existed 10xATAC libs.

Can you check why the share data link for this one is not working? http://epigenomics.sdsc.edu/zhc268/lims_singlecell/q51CaPg8_JYH_813

[brandonGonzalez01]

I am thinking it doesn't work because it was symbolic linked to the wrong path, when it was scATAC-seq it was linked to the scRNA dir. I need to delete the link in the html document and the symbolic link in the /zhc268/lims_singlecell/

[biomystery]

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