In previous genomics classes we obtained indexes with extension ",. HT2" and in the assignment for the current class I have to quote "Perform an alignment using the R package for HISAT2. Use the index built in the
previous class. (hisat2())''but I get an error.
My code:
input_file <- "C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB"
reference_index <- list.files(dane, pattern = "\.ht2", full.names = TRUE)
alignment_options <- "--score-min L,0,-0.6"
sequences <- readFastq(input_file)
alignment_result <- hisat2(sequences = sequences, index = reference_index, options = alignment_options)
error:
Error: Input/Output
file(s):
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.1.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.2.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.3.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.4.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.5.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.6.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.7.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.8.ht2
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/out.sam
C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/out.sam.txt
message: unexpected empty line C:/Users/Agatka/Desktop/ROK3/AB/ngs 3/indeksy do AB/index.1.ht2:12
how to solve such an error?