barcodes in reads_HiSeq

[narcis]

How to identify all of the barcodes in the file (using shell commands)? while the barcodes are not in the header, how to understand where they are in the read?

[GenoMax]

Are you interested in identifying where "inline" barcodes are in a read? Normal illumina barcodes are never part of the actual reads.

[narcis]

Thank you GenoMax!
Yes, I think the barcodes are not part of the reads. But, how can I make sure if they are "inline" and if they are not part of the actual sequence, then are they in another file?
I don't have the barcode sequences used for multiplexing, is it possible to demoltiplex the reads without specifying barcodes?

[GenoMax]

If standard illumina barcodes were used then they were automatically considered when the samples are demultiplexed. Look at the headers from the sequence ID of the files you have and check if the barcodes are in the ID header (http://en.wikipedia.org/wiki/FASTQ_f...ce_identifiers).

If they were "inline" then you would need to know what they were before you can start looking for them or use that information for demultiplexing.

[sphil]

Thank you GenoMax!
I don't have the barcode sequences used for multiplexing, is it possible to demoltiplex the reads without specifying barcodes?

Nope it is not.


Ask your sequencing center to provide the sequences than you can look for it.

[narcis]

Thank you GenoMax and sphil!
I will provide the barcode sequences then to demultiplex the reads.