Extract reads according to selected indexes (MiSeq))

[nazen]

Hi all!
I'm a new in bioinformatics. I have some questions about MiSeq data analysis. I have demultiplex data namely index fastq files, R1 and R2 fastq files. I need extract paired-reads according to selected indexes. Why? Because there are several different degenerate sequences of indexes and I would like to extract and analysis them separately. How is it possible to do? May be somewhere is there scripts ????
I'll really thankful for any help!

[seb567]

Indexed reads generated with the Illumina MiSeq can be demultiplexed with Illumina CASAVA. There is an option is CASAVA to change the maximum number of mismatches to support these degenerate sequences.


See these scripts for an example on how to use configureBclToFastq.pl from CASAVA.

https://github.com/sebhtml/FastDemultiplexer/blob/master/Comparison-With-CASAVA/Demultiplex-with-CASAVA-augmented.sh

Hi all!
I'm a new in bioinformatics. I have some questions about MiSeq data analysis. I have demultiplex data namely index fastq files, R1 and R2 fastq files. I need extract paired-reads according to selected indexes. Why? Because there are several different degenerate sequences of indexes and I would like to extract and analysis them separately. How is it possible to do? May be somewhere is there scripts ????
I'll really thankful for any help!

[nazen]

Seb, thanks a lot for your replay. I've installed CASAVA it works pretty good!