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boutroslab / CRISPRAnalyzeR

CRISPRAnalyzeR: interactive analysis, annotation and documentation of pooled CRISPR screens
GNU General Public License v2.0
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Streamline Setup Screen #16

Closed DarioS closed 7 years ago

DarioS commented 7 years ago

Would it be possible to make the setup quicker, by adding a set of radio buttons to the Upload Your sgRNA Library File in the screen setup section ? That would remove the need for users to download a file from the server then to upload it back to the same server again for datasets using the common screening libraries. It would also allow values to settings like Gene Identifier for non-targeting control(s) to be set to suitable defaults by the application. Otherwise, biologists will need to extract the controls from the design spreadsheet and make them comma-separated, which could take time, depending on their programming skill.

jwinter6 commented 7 years ago

Hi Dario, That's a good point. I am already working on this for the next major update since a couple of people mentioned this. I plan also to bring defaults for all addgene available pooled libraries.

Best Jan

Am 17. M?rz 2017 03:00:22 schrieb DarioS notifications@github.com:

Would it be possible to make the setup quicker, by adding a set of radio buttons to the Upload Your sgRNA Library File in the screen setup section ? That would remove the need for users to download a file from the server then to upload it back to the same server again for datasets using the common screening libraries. It would also allow values to settings like Gene Identifier for non-targeting control(s) to be set to suitable defaults by the application. Otherwise, biologists will need to extract the controls from the design spreadsheet and make them comma-separated, which could take time, depending on their programming skill.

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jecorn commented 7 years ago

Along these lines, would it be possible to allow users to enter their own regex for custom library definition files? (rather than choosing from a drop-down)

jwinter6 commented 7 years ago

Hi Jacob,

you can delete the entries in the dropdown menu - and enter your own. This can be done for FASTA and FASTQ regular expression.

ca_userregex

Is this what you refer to?

Best Jan

DarioS commented 7 years ago

Currently for GeCKO V2, it's necessary to process Library A files, get a set of count files and evaluate QC metrics, process Library B files, get a second set of count files and evaluate QC metrics, concatenate the libraries using the command line, upload the concatenated count files to CRISPRAnalyzeR and then at last do tasks like differential expression analysis. This could be streamlined by specially handling A and B library files for this screen to avoid having to merge files outside of the application.

jwinter6 commented 7 years ago

added in V1.20