ConvertToPE_BAM {MACPET} | R Documentation |
Stage 2 in MACPETUlt
needs a paired-end BAM file to run. This can be
created in Stage 1 using the usable_1 and usable_2 fastq files
created in Stage 0. However the user might have two single-end
BAM files already created but not paired (by filtering with another way than that in Stage 0 or
mapping using another algorithm than that in Stage 1)
and only needs to run Stages 2 and 3 in MACPETUlt
.
ConvertToPE_BAM
can be used on the two BAM files for pairing them, and the
resulted paired-end BAM file can then be used in Stage 2 in MACPETUlt
.
ConvertToPE_BAM(S1_AnalysisDir = "", SA_prefix = "MACPET", S1_BAMStream = 2e+06, S1_image = TRUE, S1_genome = "hg19", BAM_file_1 = "", BAM_file_2 = "", S1_makeSam = FALSE)
S1_AnalysisDir |
The directory where the resulted paired-end BAM file will be saved. |
SA_prefix |
see |
S1_BAMStream |
see |
S1_image |
see |
S1_genome |
see |
BAM_file_1 |
The directory of the BAM file with the first reads. Their Qnames have to end with /1. |
BAM_file_2 |
The directory of the BAM file with the second reads. Their Qnames have to end with /2. |
S1_makeSam |
see |
The BAM files BAM_file_1
and BAM_file_2
do not need to
be sorted, but their Qnames have to end with /1 and /2 respectively.
Furthermore, the BAM files have to include the header section.
A paired-end BAM file named SA_prefix_MACPET_Paired_end.bam
and
its index, saved in S1_AnalysisDir
.
Ioannis Vardaxis, ioannis.vardaxis@ntnu.no
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.
MACPETUlt
, SampleChIAPETDataRead_1.bam
,
SampleChIAPETDataRead_2.bam
requireNamespace('ggplot2') #Create a temporary forder, or anywhere you want: S1_AnalysisDir=file.path(tempdir(),'MACPETtest') dir.create(S1_AnalysisDir)#where you will save the results #directories of the BAM files: BAM_file_1=system.file('extdata', 'SampleChIAPETDataRead_1.bam', package = 'MACPET') BAM_file_2=system.file('extdata', 'SampleChIAPETDataRead_2.bam', package = 'MACPET') SA_prefix='MACPET' #convert to paired-end BAM: ConvertToPE_BAM(S1_AnalysisDir=S1_AnalysisDir, SA_prefix=SA_prefix, S1_BAMStream=2000000, S1_image=TRUE, S1_genome='hg19', BAM_file_1=BAM_file_1, BAM_file_2=BAM_file_2) #test if the resulted BAM is paired-end: PairedBAM=file.path(S1_AnalysisDir,paste(SA_prefix,'_Paired_end.bam',sep='')) Rsamtools::testPairedEndBam(file = PairedBAM, index = PairedBAM) bamfile = Rsamtools::BamFile(file = PairedBAM,asMates = TRUE) GenomicAlignments::readGAlignmentPairs(file = bamfile,use.names = FALSE, with.which_label = FALSE, strandMode = 1) #-----delete test directory: unlink(S1_AnalysisDir,recursive=TRUE)