I am using Rsubjunc to process my RNA seq data for DEseq2 and differential splicing analysis. I have a question about how to set multi-mapping reads alignment in Rsubjunc R package. The command I used is attached to the end of this post, the log of this command indicates that the "Max alignments per multi-mapping read" is 1 . How can I set the "Max alignments per multi-mapping read" to 300 and only the best-aligned locations (with no or fewest mismatches) are reported?
The command I use is below:
#Alignment for ctrlKO4, sort and index: subjunc("~/Documents/Xiao/RNAseq/hg38_index/BSgenome.HSapiens.UCSC.hg38.mainChrs", readfile1 = "./1-ctrlKO4_R1_001.fastq.gz", readfile2 = "./1-ctrlKO4_R2_001.fastq.gz", output_file="ctrlKO4.bam") library(Rsamtools) sortBam("ctrlKO4.bam", "ctrlKO4_sorted") indexBam("ctrlKO4_sorted.bam")