Hi! I ran Trimmomatic on paired end reads which, as I understand, is supposed to yield 1_paired, 1_unpaired, 2_paired, and 2_unpaired fastq files. However, after the process was completed, my 2_paired file seemed empty, as the font of the other files were colored red and when I ran a FASTQC on these files, I was only able to get reports for the other three files, but not the 2_paired file. Does this happen sometimes? Should I just proceed with mapping/alignment with just the 1_paired fastq file? Thank you!
Hi! I ran Trimmomatic on paired end reads which, as I understand, is supposed to yield 1_paired, 1_unpaired, 2_paired, and 2_unpaired fastq files. However, after the process was completed, my 2_paired file seemed empty, as the font of the other files were colored red and when I ran a FASTQC on these files, I was only able to get reports for the other three files, but not the 2_paired file. Does this happen sometimes? Should I just proceed with mapping/alignment with just the 1_paired fastq file? Thank you!