Final debugging on Demul_trim_prep

Doing final checks to make sure the Demul_trim_prep workflow is OK on Mac OSX:

-Former .Z error now seems to be fixed with zcat workaround
-Had to change line breaks on the barcode mapping files to Unix (LF)
-Had to install Flash v1.2.6 (downloaded from here) – unzipped tar.gz and executed “make” command inside directory. Then moved compiled binary to /usr/bin directory on my MacAir

Test command seemed to work fine (although the reads were merged with 50 bp overlap, and shouldn’t have been…):

perl Demul_trim_prep.pl /Volumes/Holly_1TB/GOM_Illumina/demul_trim_prep/input_files/KO_1_dtp/ /Volumes/Holly_1TB/GOM_Illumina/demul_trim_prep/demul_trim_prep_mappingfiles/1926_KO_1_QIIME_mapping_DemulTrimPrep.txt /Volumes/Holly_1TB/GOM_Illumina/demul_trim_prep/demultiplexed/ KO_1_dtp
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