countReads: countReads
In scottzijiezhang/MeRIPtools: Analyze MeRIP-seq data and QTL calling

This is the very first function in MeRIP-seq data analysis that initianize a 'MeRIP' object. This function takes BAM files of Input/IP library of each samples as input and use given GTF file as gene annotation to divide genes into consecutive bins of user defined size.

countReads(samplenames, gtf, fragmentLength = 150, bamFolder,
  outputDir = NA, modification = "m6A", binSize = 50,
  strandToKeep = "opposite", paired = FALSE, threads = 1,
  saveOutput = T)

`samplenames`	The names of each sample (prefix for bam files).
`gtf`	The gtf format gene annotation file
`fragmentLength`	The RNA fragment length (insert size of the library).
`bamFolder`	Path to the folder where bam file locates
`outputDir`	The directory to save output files
`modification`	The modification used to name the BAM files.
`binSize`	The size of consecutive bins to slice the transcripts
`strandToKeep`	According to library preparation protocol, choose which strand to count. Stranded RNA library usually seq the "ooposite" strand. Small RNA library seq the "same" strand.
`paired`	Logical indicating whether the input bam files are from paired end sequencing. Default is FALSE. If using paired end data, the read length will be estimated from the data and only good mate are counted.
`threads`	The number of threads to use for hyperthreading
`saveOutput`	Logical option indicating whether to save output as an RDS file.