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Old 06-11-2012, 01:58 PM   #1
kga1978
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Location: Boston, MA

Join Date: Nov 2010
Posts: 100
Question IlluminaBasecallsToSam - specify directory with _barcode.txt files?

Hi All,

I am demultiplexing HiSeq and MiSeq runs using Picard. I have read access to the BaseCalls directory, BUT I can't write to it. Hence when I run 'IlluminaBasecallsToSam' I need to specify some other directory where I can write my _barcode.txt files. For example:

Code:
java -Xmx2g -jar /seq/software/picard/current/bin/ExtractIlluminaBarcodes.jar BASECALLS_DIR=<bustard directory> OUTPUT_DIR=<_barcode.txt directory> ...
I can run this command, no problem. However, when I next need to run 'IlluminaBasecallsToSam' to get my SAM files, this program expects the _barcode.txt files to be in the BaseCalls directory and I don't seem to be able to specify a separate directory where it can find the barcode files - i.e. there is no way (as far as I can see) in IlluminaBasecallsToSam to specify the OUTPUT_DIR from ExtractIlluminaBarcodes.jar??

The only way I seem to be able to get around this is to first copy all the flow cell data to a separate directory where I DO have write access, but that takes A LOT of space and I/O - especially from a HiSeq run. Surely there must be a better way around this problem?

Please help - thanks in advance for all the great suggestions ;-)
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