Hello!
I have used Bowtie2 to in the past successfully to index and align reads on R. I currently have a job that requires using large index. bowtie2_build returns successful index, but it has the unique bt2l extension (as mention in bowtie2 manual).
However, when I attempt to use this index for aligning using the bowtie2 function, the index is rejected because it's not a .bt2 extension:
-- bowtie2(bt2Index = "mm10.hg38_bowtie2", samOutput = "dspt5_1.sam", seq1 = "dspt5_1.fastq", seq2 = "dspt5_11.fastq", overwrite = FALSE)
-- Error in checkFileExist(paste0(bt2Index, ".1.bt2"), "bt2Index") :
--- For argument bt2Index, file does not exist: mm10.hg38_bowtie2.1.bt2
I have attempted to find way to let bowtie2 know that I am using a large index (.bt2l), but couldn't. Anyone knows how I could get around this?
Thank you!!
