Batch Files Explained
Batch files are a quick and easy way to add parameters to files when processing multiple at once.
When uploading multiple files using the 'Batch Upload' tab, CRISPResso checks to see if you provided an optional batch file, then uses the information stored inside while processing.
This additional information could include amplicons, sgRNA, edits to the quantification window, and more. For a full list, visit the CRISPResso2 README.
Before We Begin:
If you have external fastq files stored on Amazon AWS, creating an S3 Batch File will allow you to download and process those files.
In order for this to work, you'll first need to have setup an S3 Connection and given yourself S3 User Access in the Admin panel. If you don't have access to the admin page, you can ask your IT department for help in creating the S3 connection, and setting up your user access.
The rest of this tutorial will assume that you've already set up this external access in the admin panel.
Download Example File:
Download an example s3 batch fileAfter you've downloaded this tsv file, you should open it in a spreadsheet editor. This tutorial will assume you're using Microsoft Excel or Google Sheets, but any text editor should work.
This is what you should see:
Edit File
Inside the spreadsheet editor, you should replace the values with the values of your files. The fastq_r1 fields should be replaced with the URLs of your samples. If you are not doing paired-end reads, delete the fastq_r2 column.
The only mandatory fields are names and fastq_r1, but you can also input your amplicon into the a column, and your sgRNA into the g column.
Here is an example of what a paired-end read file might look like:
Exporting your saved file
Finally, you can save or download your edited file inside of the File menu. You should save the file as either a .tsv, .csv, xls, or xlsx file type.
Download Example File:
Download an example batch fileAfter you've downloaded this tsv file, you should open it in a spreadsheet editor. This tutorial will assume you're using Microsoft Excel or Google Sheets, but any text editor should work.
This is what you should see:
Edit File
Inside the spreadsheet editor, you should replace the values with the values of your files. The fastq_r1 and fastq_r2 fields should be replaced with the exact filenames of your samples that you will either upload individually, or as a part of a zip file. If you are not doing paired-end reads, delete the fastq_r2 column.
The only mandatory fields are names and fastq_r1, but you can also input your amplicon into the a column, and your sgRNA into the g column.
Here is an example of what a paired-end read file might look like:
Exporting your saved file
Finally, you can save or download your edited file inside of the File menu. You should save the file as either a .tsv, .csv, xls, or xlsx file type.
