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| library(Rsubread) buildindex(basename='my_index', reference='genome.fa') align(index='my_index', type='dna', readfile1='reads.txt.gz', output_file='rsubread.bam', nthreads=5, indels=16, unique=F, nBestLocations=3)
align(index='my_index', readfile1='reads1.fq.fz', readfile2='reads2.fq.gz', type='dna', output_file='rsubread.bam', minFragLength=50, maxFragLength=600)
subjunc(index='my_index', readfile1='rnaseq-reads.txt.gz', output_file='subjunc_results.bam')
featureCounts(files="mapping_results_SE.sam", nthreads=5)
featureCounts(files="mapping_results_SE.sam",annot.ext="annotation.gtf", isGTFAnnotationFile=TRUE,GTF.featureType="exon",GTF.attrType="gene_id")
featureCounts(files=c('read1_mapped.bam', 'read2_mapped.bam')) featureCounts(files='PE_mapped.bam', isPairedEnd=T, requireBothEndsMapped=TRUE, countChimericFragments=FALSE)
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