demultiplexing Nextera Rapied Capture exome data on bcl2fastq 1.8.3

[wintergreen36]

I am using bcl2fastq 1.8.3 on ubuntu 14.04 LTS.

What's the best variable can be given for demultiplexing Nextera Rapied Capture exome data

details

Next era indice - 8 bases
RUN TYPE - read 1(100 cycles), read 2(8cycles) , read 3(100cycles),

[GenoMax]

What's the best variable can be given for demultiplexing Nextera Rapied Capture exome data

Not sure I understand the question. You will have to clarify further.

[wintergreen36]

I tried to demultiplex nexera exome data with a normal command , it gave an error like barcode lenght including delimter is 7

so I gave varibale like Y100n,I8,Y100n is this correct ?

[GenoMax]

Use bases mask is generally determined automatically from the RunInfo.xml file.

You can use Y100n,I7n,Y100n or edit your samplesheet and make the tags 7 bp long.

[wintergreen36]

@genomax is there any wrong if we declared index as ,I8

[GenoMax]

Last base in the read (even for tags) is generally not considered (because it lacks phasing information). So when bcl2fastq/CASAVA demultiplexes a run it will use n-1 cycles for demultiplexing. You can use an appropriate "--use-bases-mask" or adjust your samplesheet when setting up a demultiplexing run. If you need 8 bases on the tag reads then set sequencing run for 9 cycles.