Question: Barcode Splitter On Paired End Reads
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Veranja Liyanapathirana • 70 wrote:
Dear Galaxy team,
I am sorry for repeatedly asking this question but I would like some
feed back from anyone who has used barcode splitter on paired end
reads as the different alternatives I used do not give satisfactory
results in terms of expected read alignments.
I have a set of Illumina Miseq reads with inhouse barcodes that I need
to de maultiplex.
It is esstential to make sure that the read 1 and read 2 are split to
the same group and in instances that this condition is not fulfilled,
the reads to be discarded.
I tried to
1. Join read 1 and read 2 and then run barcode splitter, followed by
FASTQ splitter
2. Use barcode splitter on read 1 and read 2 separately and use FASTQ
joiner on the results to exclude instances where R1 and R2 are in
different reads followed
3. Use barcode splitter on R1 and R2 results and straightaway use
Bowtie for illumina for mapping
The results I get in the three methods are not compatible with each
other. I would like to know the best method from the experience of
other users on what the best method using Barcode splitter on Illumina
Paired end reads,
Thank you,
Kind Regards,
Veranja
Veranja Liyanapathirana
Graduate Student
CUHK