Fixed: Read counts for samples on single lane

SciLifeLab / bcbb

Useful bioinformatics code, primarily in Python and R

http://bcbio.wordpress.com

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Closed remiolsen closed 10 years ago

remiolsen commented 10 years ago

When demuxing samples with 'NoIndex' it will do so twice. First the indexes (--use-bases-mask N101, Y8, N101), then the reads only (Y101, N8, Y101)
Indexes become 'read1' and 'read2'. Moved them to I1 and I2
configureBcl2Fastq using --force for the reads only demuxing to overwrite Makefile