Changes

== Introduction ==

== Introduction ==

'''NOTE: the current version works only for single end reads'''

'''NOTE: The current version works only for single end reads. If the input bam file contains paired end sequences, reads from the same fragment will be counted independently'''

* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC content of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

* This tool was initially developed for RNA-seq data to quantify gene/exon expression but can also be used for other purposes as well.

* This tool was initially developed for RNA-seq data to quantify gene/exon expression but can also be used for other purposes as well.