multi-mapping reads settings in Rsubread or Rsubjunc

Question

[xiaoleiusc]

Hi All,

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?

Thanks ahead,

Xiao

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")

[GenoMax]

Looking at the subread manual you will need to add following options

--multi-mapping -B 300

[xiaoleiusc]

Thank you GenoMax! I am new to R, do you mean to keep my script the same but add --multi-mapping -B 300 after subjunc and before the parenthesis?