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Old 08-12-2014, 04:45 AM   #1
wintergreen36
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Default Demultiplexing with last three bases

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.
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Old 08-12-2014, 04:55 AM   #2
GenoMax
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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.
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Old 08-12-2014, 05:01 AM   #3
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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
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Old 08-12-2014, 05:07 AM   #4
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--use-bases-mask nnnYYY.

Last edited by GenoMax; 08-12-2014 at 05:10 AM.
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Old 08-12-2014, 05:12 AM   #5
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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 ?
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Old 08-12-2014, 05:21 AM   #6
GenoMax
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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.

Last edited by GenoMax; 08-12-2014 at 08:27 AM.
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Old 08-12-2014, 06:57 AM   #7
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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
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Old 08-12-2014, 09:07 PM   #8
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Thank You very much @ Genomax @ westerman
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Old 08-12-2014, 09:57 PM   #9
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@ hi genomax and westerman , which version of ubuntu u experienced best to installa and run casava and bcl2fastq :-)
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Old 08-13-2014, 03:06 AM   #10
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Quote:
Originally Posted by wintergreen36 View Post
@ 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.
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