Multiplex/DeMultiplexing of illumina RNAseq Single End

Question

[Jonathan Crowther]

Is there a way to identify if the RNASeq data has already undergone demultiplexing?

I have received files which have been run on 4 lanes and so I have 4 .fastq.gz files for each sample.

I know I can compare the qualities of these to ensure there is no lane specific bias but can I figure out from these files if they have been demultiplexed?

Also in terms of merging the files should I run FastQC on each file prior to merging and again after? I am trying to find a nice tutorial on demultiplexing so if anyone could recommend one I would really appreciate it.

I have normally just received a demultiplexed .fastq.gz file and am now trying to learn how to handle the data I have from basespace.

Cheers and Happy Holidays.

Answer 1

[Istvan Albert]

In most current techniques demultiplexing takes place automatically during the instrument's data post-processing protocols. The information is typically available either in the read's name or some other supporting information.

For example the Illumina read naming contains information on the index:

http://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers