Analyzing Chip Seq Data From ENCODE

Question

[Thanos Sakavelis]

Hello everyone,

I am studying bioinformatics and as an amateur I'd like to ask you a few questions. Right now I am focusing in a chip-seq experiment from Encode.I've downloaded the raw data from both biological replicates,I've done quality check via the Fastqc program and I've finished the mapping procedure against the reference genome (Mus Musculus).The output of the mapping was a sam file that I converted to bam via the samtools program in order to utilize it to the peak calling algorithm.Here is my issue!As I read the macs algorithm has the option to use as a parameter a control sample together with the treatment sample for finding more reliable peaks.Where can I find the control data in Encode?The chip-seq experiment I am talking about can be seen from the below url: https://www.encodeproject.org/experiments/ENCSR985ZTV/ At first, I used the alignments in bam format in the field of processed data.Then, I noticed that in the summary of the experiment there is an option named "Controls" and so here I am!This is the link for the control data: https://www.encodeproject.org/experiments/ENCSR601HSS/ Here I can see only one replicate.Could you please help me with this issue because I am really confused!

Thank you in advance for your help :)

Answer 1

[Devon Ryan]

ENCODE had a penchant for using the same control sample for multiple things. In this case, there really is only a single control sample for both CTCF IPs, so just use that for peak calling both IP BAM files.

Answer 2

[Thanos Sakavelis]

Thank you Devon for your response.Could you please tell me the exact name (accession code) of the control sample that I should use as control?

[GenoMax]

Please use ADD COMMENT/ADD REPLY when providing additional information/replying to existing posts. SUBMIT ANSWER should only be used for new answers to original question. This comment belong up against @Devon's post.

[Devon Ryan]

It's the one you linked to (ENCSR601HSS).

[Thanos Sakavelis]

Yes of course but which exact file?The processed unfiltered bam file (ENCFF040OST) or the filtered one(ENCFF574XMX)?

[Devon Ryan]

Since you aligned the IP samples yourself, get the fastq file and process it the same way.

[Thanos Sakavelis]

Ok now it is clear!Thank you very much indeed!

[Thanos Sakavelis]

Should I use the same parameters that I used at the first mapping (treatment samples) or more "relaxed"? Thank you

[Devon Ryan]

Use the same settings.

[Thanos Sakavelis]

Thank you very much Devon!