Hi all, I am looking to map my pair-ended trimmed reads to my reference genome using Bowtie2. I input the R1 and R2 fastq files and the reference genome FASTA file. It gives me the below error and I am not sure how to fix this.
Error, fewer reads in file specified with -2 than in file specified with -1 Error, fewer reads in file specified with -2 Error, fewer reads in file specified with -2 than in file specified with -1 than in file specified with -1 Error, fewer reads in file specified with -2 than in file specified with -1 Error, fewer reads in file specified with -2 than in file specified with -1Error, fewer reads in file specified with -2 than in file specified with -1
Error, fewer reads in file specified with -2 than in file specified with -1 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' terminate called recursively terminate called recursively (ERR): bowtie2-align died with signal 6 (ABRT)
The R1 and R2 reads are definitely same size and I also have enough space left on my galaxy for analysis.
Any help much appreciated on how I can fix this please?
Have you trimmed these files and not used paired-end mode eventually?
Hi! Have you tried to count the number of reads in each file? You could try some of the answers suggested at How to count fastq reads.
Size is not an indicator for number of reads. Did you process these reads somehow, like trimming? A common rookie mistake is trimming PE data with a non-PE trimmer, causing unsynced files.