Demultiplexing with last three bases

[wintergreen36]

What's the possibility of using the last three bases in the index for demultiplexing the HiSeq 2500 data using bcl2fstq

Let me say index is GCATCG
I wish to de multiplex using the last three bases TCG only ,
The quality scores for index read were bad; it's 40 %

how to give a variable for serving the above said purposes.

[GenoMax]

You can check (even by eye) to see if that is possible by looking at the indexes you actually used. If two or more overlap (in last three bases that you want to use) then you won't be able to demultiplex.

[wintergreen36]

yaya am aware of that , let me say

every lane got 6 samples without overlapping the last three bases ,
if its a simple 50 SR run , how to write a varibale to mask the first three bases and demultiplexing using only last three bases

[GenoMax]

--use-bases-mask nnnYYY.

[wintergreen36]

Below command line includes the path too see the last line

/usr/local/bin/configureBclToFastq.pl --input-dir /media/vanessa/Sandor_1/20140408SANDORSR50/140408_700417L_0315_BC4C4GACXX/Data/Intensities/BaseCalls --output-dir /media/vanessa/Sandor_1/Unaligned --sample-sheet /media/vanessa/Sandor_1/20140408SANDORSR50/140408_700417L_0315_BC4C4GACXX/Data/Intensities/BaseCalls/SampleSheet.csv --USE_BASES nnnYYY
will it work like this ?

[GenoMax]

Please see the updated command option in post #4. Should be --use-bases-mask nnnYYY.

Forgot about Read 1. Rick has provided the correct full syntax below.

[westerman]

GenoMax undoubtedly has the syntax correct for a single-end demultiplex [I mostly do paired-end] but it is possible that you may need the full specification of

use-bases-mask=Y*,InnnYYY

or maybe

use-bases-mask=Y*,InnnYYYn

[wintergreen36]

Thank You very much @ Genomax @ westerman

[wintergreen36]

@ hi genomax and westerman , which version of ubuntu u experienced best to installa and run casava and bcl2fastq :-)

[GenoMax]

@ hi genomax and westerman , which version of ubuntu u experienced best to installa and run casava and bcl2fastq :-)

Exact version of ubuntu should not matter as long as the software works.