Hello, I am newbi in processing fasq files, but it is the first time that happened to me. I downloaded the L00N_RN_00N.fastq.gz, and joined in two fastq files (i.e. _R1.fastq.gz and _R2.fastq.gz). Then I load the genome reference to memory and I make a loop samples for BWA, but today I have an error message:
> [mem_sam_pe] paired reads have different names
And this is my code that I used.
call('bwa mem -t' + str(args.threads) + ' -R "@RG\tID:' + sample_name + '\tLB:library\tPL:illumina\tPU:library\tSM:' + sample_name + '" ' + genome_ref + ' ' + forward_paths[i] + ' ' + reverse_paths[i] + ' > ' + sample_path + '/' + sample_name + '_bwa.sam',shell = True)
I am quite confuse, because I have analyse several samples as always but I've never seen that. Any help is welcome! :) I downloaded the files again and joined them.