I've a little problem to understand the scripture command line :
So I've the accepted_hits.bam for all my samples. So I have to merge all the bam files into one big bam file before running scripture. In the help file there is two alignment file param :
Which one do I have to use to input the merged bam file ?
Here's the help file :
Parameters -alignment <Alignment file in BAM, SAM or Alignemnt format> -maskFileDir <Mask File directory> -out <Output file name> -windows <Comma separated list of windows to evaluate> -sizeFile <Chromosome size file> Optional arguments: -trim <Include this flag if trimming of the ends of windows based on read coverage is desired this is expensive> -alpha <Desired FDR> one of -chr <Chromsomosome to segment> or -chrSequence <Necessary to filter spliced reads by splice site information. Notice that this is only compatible with region files that contain regions of only one chromosome> -dontFilterCanonicalSplice -start <To segment only a subregion of the chromosome include its start> -end <To segment only a subregion of the chromosome include its end> -minSpliceSupport <Minimum count to support splice reads, default is 1> -pairedEnd <Paired end alignment files> -strandSpecificReads <Strand specific alignment file> -scoreRegions <Full BED to score> -upWeightSplices -lambda <If a prior background expectation for number of reads per base exists> -exons <BED file of exons> -introns <Introns and counts> Task: AddPairs - Uses a paired end alignment to tune graph -in <Graph in .dot format. Standard input is assumed> -pairedEnd <Paired end information (as in previous task), in single line BED format> -maskFileDir <Directory containing mask files for the genome> -chr <Chromosome (only a chromosome at a time is supported at this point)> -sizeFile <Chromosome size file> -out <Output file name> Task: score - Computes several expression related scores for a set of annotations -in <Full BED file with annotations to score> -alignment <Alignment file in BAM, SAM or Alignemnt format> -sizeFile <Chromosome size file> -out <Output file name> -maskFileDir <Mask File directory>