Can handle 10xRNA

in both:

• Seqmanager for demultiplex
• scAPP for processing by calling cellranger

Encode function tested for atac and atac_chip

include delete ENCODE temp fastq files

add encode function

In metaData and SetQC apps

10x(TA) demux can handle customized mask

v5.2

solved extra pars in 10x demux for masking

Add singlecell app + bulk edits

1. added single cell app
2. added bulk edits tab for meta data app

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Finished integrating 10x ATAC into our LIMS.

example

http://epigenomics.sdsc.edu:8000/setqc/597/

The last column TenX Processed is showing the status of 10x cellranger pipeline. If shown Yes there, you can click the Yes and open the web_summary.html from 10x pipeline and share the link with colaborators.

Important:

If you want input 10x-ATAC libraries into your LIMS, please redownload the template.xlsx and select Experiment type as 10xATAC. Otherwise, the LIMS won’t recognize it is a 10x library.

Any other things changed?

No. As long as you import your library as 10xATAC, you can do the same setQC request. The 10x pipeline will automatically added and the results will display in the detail page of the setQC, similar to http://epigenomics.sdsc.edu:8000/setqc/597/

Acknowledgement

@brandon Gonzalez - contribute the most of the work
@olivier
@Yuxin (edited)

Handle 10x ATAC in setQC app

1. Able to qsub 10x cellranger jobs for 10xATAC libs in a setqc

Decoupled from Google Spread sheet

With this version release, we formally disconnected our LIMS with our previous Google Spreadsheet tracking systems. Now:

1. The LIMS is providing a template.xslx for users to craft any information they want to input into our LIMS. Simply copy & paste will do the job of input data into LIMS.

2. The LIMS is also providing an export function to export all user's metaData in one Excel file. The exported excel file contains the same sheets and the same columns as template.xslx, only lacking of validation part.

3. We've finished all comparison between GS and LIMS to make sure there is no data lost or changed between the OLD and NEW system.

launched admin app to handle collaborators.

4.0

confirm delete phone app

snATAC_V2 demux capability

v3.2

fixed a bug in show Mysample/lib/seq details'

setQC run pipeline (fastq,atac,chip-seq)

• with preview function