Are Barcodes always on R1 and Sequence data on R2?
Question: Are Barcodes always on R1 and Sequence data on R2?
No, it really depends on the protocol. In some protocols this convention is swapped, in others the barcodes can be distributed across both reads.
How do I know what protocol my data was sequenced with?
Question: How do I know what protocol my data was sequenced with?
If you have 10x data, then you just need to count the length of the R1 reads to guess the Chromium version (see this tutorial). For other types of data, you must know the protocol in advance, and even then you must also know the multiplexing strategy and the list of expected (whitelisted) barcodes. The whitelist may vary from sequencing lab to sequencing lab, so always ask the wetlab people how the FASTQ data was generated.
When something goes wrong in Galaxy, there are a number of things you can do to find out what it was. Error messages can help you figure out whether it was a problem with one of the settings of the tool, or with the input data, or maybe there is a bug in the tool itself and the problem should be reported. Below are the steps you can follow to troubleshoot your Galaxy errors.
Expand the red history dataset by clicking on it.
Sometimes you can already see an error message here
View the error message by clicking on the bug icongalaxy-bug
Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
Expand the history item
Click on the details icon
Scroll down to the Job Information section to view the 2 logs:
