Hi all, I have a question regarding paired end FASTQ files for chip-seq analysis. Which following step is better to start with? 1) With FASTQ joiner to join 2 paired end FASTQ files or 2) Directly align in Bowtie2 using 2 different files? (also, in bowtie what is the best option for Do you want to set paired-end options ? Y/N)
Once I get the aligned files, in next step ( MACS2 callpeak option) what option I should pick? Are your inputs Paired-end BAM files? Y/N (as we have already made single file for paired end files, is it necessary to opt YES for this?).
I really appreciate your valuable answers, thank you.