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 
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