Question: Barcode Splitting
gravatar for Rajarshi Ghosh
6.0 years ago by
Rajarshi Ghosh10 wrote:
I have lllumina sequences which are barcoded in the sequence identifier e.g.: @FCC186GACXX:6:1101:1473:2060#TCGCAGGA/1 CTCCACGAAACCGGAAGGGTAGAAAAGTTCGGTCAACTCGTTCCTCACAATTTGCCCGATTCTCAGAAAA ATTGTTTTGTGACCTCTCTC The '#TCGCAGGA" is the barcode. As the barcode is not on the 5' or 3' end I cannot use the barcode splitter. Is there a workaround in Galaxy for this? Thanks!
galaxy • 1.4k views
ADD COMMENTlink modified 6.0 years ago by Jennifer Hillman Jackson25k • written 6.0 years ago by Rajarshi Ghosh10
gravatar for Philipe Moncuquet
6.0 years ago by
Philipe Moncuquet40 wrote:
Hi, How comes the barcode not be at 5' or 3' end, do you have primer sequences or stuff like that ? The barcode you show cannot be found in the sequence you show... I know that FastqMCF is an alternative tool that can be found in the toolshed and that deals with barcode. Philippe 2012/12/3 Rajarshi Ghosh <>
ADD COMMENTlink written 6.0 years ago by Philipe Moncuquet40
gravatar for Jennifer Hillman Jackson
6.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Rajarshi, How many barcodes do you have? If just a few, then the 'Filter and Sort -> Select' tool might be a good choice. This will do about the same thing as the "grep" in the top answer at Biostar, for the same type of question: I did check the tool shed and didn't find any tools that would do this. Maybe also post a inquiry and see if someone has developed a tool that will demultiplex fastq sequences with barcodes in the identifier, but hasn't loaded it into the tool shed yet? You could also open a request to have such a tool created (or the current barcode tool expanded): Good luck! Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.0 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour