Hi. I received the fastq files for my ChIP-seq studies. We did 50 bp paired-end.

I am new to the NGS. I used paired-end data from public files and usually, there were only two fastq files for the two reads.

Now, I received the file. 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"m 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.

Note that if files are specified using -1/-2, a file cannot

also be specified. Please run bowtie separately for mates and singles.

Error: Encountered internal Bowtie 2 exception (#1)

I"m also unsure about the use of Paired-end merge tools.