Are these samples de-multiplexed?
1
1
Entering edit mode
6.8 years ago
Nick ▴ 290

I haven't done Illumina de-multiplxing before as the lab I am used to work with has done this by default. I'm now getting samples from a lab that says that it doesn't do de-multiplexing. It's a new lab which doesn't have experience with NGS so I am not quite sure they now what they are doing. So I got the following Illumina run (this is just a screenshot showing some of the files):

screenshot of files


The SampleSheet in this folder has the following content (again a screenshot):

samplesheet screenshot

To me it looks like the data has been already de-multiplexed as the fastq files have the same names as the samples. What do you think? How can I test whether this is, indeed, the case? Also, I see some files (their names start with "Undetermined") which are not assigned to any sample. What shall I do with them?

illumina de-multiplexing miseq • 2.5k views
ADD COMMENT
6
Entering edit mode
6.8 years ago

These are indeed demultiplexed. Providing demultiplexed files is such a simple thing for a sequencing facility to do that I'm always amazed when one is too lazy to do so. The "Undetermined" files can be ignored. I never provide those to our users. I should note, though, that I routinely check how many reads are in that file, simply because if those files are large then there was an issue with the library or sequencing.

ADD COMMENT
1
Entering edit mode

It looks like this is a MiSeq run as well, and by default De-multiplexing is part of the standard MiSeq workflow even if you don't send samples to MiSeq reporter for on-board analysis. In which case Nick you should inform them of this so they don't confuse other customers. Also, the lab in question really needs to do their homework a bit more before they start providing data to outside groups/labs...

ADD REPLY

Login before adding your answer.

Traffic: 1404 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6