I have a question about running MACS tool for my chip-seq data to call the peaks for the transcription factor binding site.
1. My data is pair-end sequenced. I have already upload the two FASTQ datasets R1 and R2 into galaxy, converted into the right format and run the Bowtie tool for mapping.
2. After mapping, I got one SAM dataset from the two FASTQ dataset.
3. When I want to run MACS tool, under the "Paired End Sequencing" option, if I select "single end", the SAM dataset in history can be recognized; however, if choose "paired end", it asks for the elandmuti format. and asks for two ChIP-seq Tag files.
4. I want to know should I choose single-end or paired-end?
5. Because my sequencing is paired-end sequencing, is that correct if I should choose single-end?
6. If I choose paired-end, how can I get the elandmuti format dataset and what are the two files the tool asks stand for? Are they the datasets from the two biological replication?
7. What is the tag size stands for?
I have no experience in bioinformatics, sorry for those stupid questions. and I appreciate for the kind reply.
Tool name: MACS
Tool version: 1.0.1
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/macs