I am new to the NGS. For training, I used paired-end data from public files, and usually, there were only two fastq files for the two reads.
Now, I receive the fastq files for my ChIP-seq studies. We did 50 bp paired-end. And for one PE file, there are four fastq files. For example:
R1F=IN1_S1_L001_R1_001.fastq R1R=IN1_S1_L001_R2_001.fastq R2F=IN1_S17_L002_R1_001.fastq R2R=IN1_S17_L002_R2_001.fastq
I am now a bit confused about how to handle these 4 data.
I tried to do bowtie2 paired-end mapping for R1F as -1 and R1R as -2 but it seems not working.
Bowtie2 notification: Note that if <mates> files are specified using -1/-2, a <singles> file cannot also be specified. Please run bowtie separately for mates and singles. Error: Encountered internal Bowtie 2 exception (#1)
I am also unsure about the use of Paired-end merge tools.
Please help. Thank you