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./readCount --reference hg19.fa --regions refFalt.exon.hg19 --min_overlap 5 --uniq --exon_out exon.readcount --gene_out gene.readcount input.bam
./readCount --reference hg19.fa --regions refFalt.exon.hg19 --min_overlap 5 --uniq --exon_out exon.readcount --gene_out gene.readcount input.bam
The following example generate normalized read counts using the number of reads that are only mapped to targets:
./readCount --reference hg19.fa --regions refFalt.exon.hg19 --min_overlap 5 --uniq --norm_by_mapped2target --exon_out exon.readcount --gene_out gene.readcount input.bam
== Input files ==
== Input files ==
