hello bioBakery community!
I am currently working on pathways project, and I have encountered an issue with certain fastq files. In order to align the two fastq files using the align() function from Rsubread the files are required to have the same amount of reads. However some of the data I want to collect have different amount of reads. here is the R code that uses the align function:
folder_path <- "{main_folder_path}"
metaphlan_database_folder <- "{metaphlan_database_folder}"
# Set the paths to your input files
buildindex(basename = "my_index", reference = "{annotation_file}")
readfile1 <- "{fastq_file_3}" # Path to the first FASTQ file
readfile2 <- "{fastq_file_4}" # Path to the second FASTQ file
annotation_directory <- "{reference_folder_path}" # Path to the annotation directory
dictionary_path <- "{dictionary_path}" # Path to the json dictionary file
# Align reads (execute only once)
align(index = "my_index", readfile1 = readfile1, readfile2 = readfile2, type = "rna", output_file = file.path(folder_path, "aligned_reads.bam"))
while trying to run on two fastq files that have different amount of reads for example: File1: 11128455 reads, File2: 10985701 reads I get the following error message: Error: Input Files have different Amount of Reads
I want to be able to run the code on these files even though they have different amount of reads, while minimizing the amount of data lost in the process. Do you have any suggestions? Is there another align function in R that does not require the fastq files to have the same amount of reads?
thank you in advance,
nadav