I've been doing Chip-seq analysis for few months now. I decided to use MACS2 for the analysis. It's a very nice tool to deal with any kind of data. But recently I've encountered with a new problem.
I got control which is single-end & treatment sample which is paired-end. In macs2 we give control & sample together for differential peak calling & we've to tell if the files are in BAMPE or BAM format. But for this situation this won't work.
So I searched for this problem in biostars itself & end up getting 2 posts - Combination Of Paired-End And Single-End Samples In Chip-Seq Tf Study Paired end and single end with MACS2
As stated by @Istvan Albert I tried merging both paired end files with fastq-join. But out of 33631672 reads only 269489 were joined. So I tried metagenomics tool ,QIIME's strategy of converting paired-end to single end which is convert reverse strand to forward strand ,by doing reverse complement of reverse read, and just doing 'cat' on forward & reverse complement files to get single file. (Note: these files were converted from FASTQ to FASTA in this process). This strategy also didn't work out and I end up getting a linear peak model.
In the second post (Paired end and single end with MACS2) it was mentioned we can just take forward read & do the analysis, which is contradictory to the first post (https://www.biostars.org/p/87138/). Can I follow this strategy ?
Please help me out. Thank you in advance :)