Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
convert base call files (*.bcl) into files (*_qseq.txt) giampe Bioinformatics 12 10-20-2011 09:45 AM
PicardTools IlluminaBaseCallsToSam Protaeus Bioinformatics 0 05-10-2011 11:06 AM
qseq files versus sequence.txt files drio Illumina/Solexa 3 11-09-2009 10:02 AM
s_#_sorted.txt files caza Bioinformatics 2 04-28-2009 09:12 AM
solexa output files | s_*_seq.txt vs. s_*_sequencece.txt lajoieb Illumina/Solexa 3 04-08-2009 06:52 PM

Thread Tools
Old 06-11-2012, 02:58 PM   #1
Senior Member
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:

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 ;-)
kga1978 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:31 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO