ChIP-Seq Preprocessing
Finding Data
Using SRA-explorer
https://www.ncbi.nlm.nih.gov/Traces/study/?acc=%20PRJNA106863&o=acc_s%3Aa
To download a txt file list of SRA IDs for a GEO DataSet, search
https://www.ncbi.nlm.nih.gov/geo using the GEO accesssion (found in the data
availability section of published papers). Click SRA Run Selector at the bottom
of the GEO accession page. In the SRA Run Selector sample table tick the desired
samples and then download the Accession List. This downloads a txt file called
SRR_Acc_List.txt which can be used as input to --public_data_ids.
Finding controls
Using Encode
Terms
Isogenic replication : Biological replication. Two replicates from biosamples derived from the same human donor or model organism strain. These biosamples have been treated separately (i.e. two growths, two separate knockdowns, or two different excisions).
Technical replication : Two replicates from the same biosample, treated identically for each replicate (e.g. same growth, same knockdown).
MEF Control
mef_files.txt
"https://www.encodeproject.org/metadata/?type=Experiment&accession=ENCSR000CBB&files.output_category=raw+data&files.output_type=reads&files.status=released"
https://www.encodeproject.org/files/ENCFF001KPR/@@download/ENCFF001KPR.fastq.gz
https://www.encodeproject.org/files/ENCFF001KPS/@@download/ENCFF001KPS.fastq.gz
xargs -n 1 curl -O -L < mef_files.txt
NP Control
ENCSR295GGT_files.txt
https://www.encodeproject.org/files/ENCFF557BAE/@@download/ENCFF557BAE.fastq.gz
https://www.encodeproject.org/files/ENCFF125ETQ/@@download/ENCFF125ETQ.fastq.gz
https://www.encodeproject.org/files/ENCFF066LAE/@@download/ENCFF066LAE.fastq.gz
https://www.encodeproject.org/files/ENCFF078PNM/@@download/ENCFF078PNM.fastq.gz
https://www.encodeproject.org/files/ENCFF202WAI/@@download/ENCFF202WAI.fastq.gz
xargs -n 1 curl -O -L < ENCSR295GGT_files.txt
ES Control
es_control.txt
"https://www.encodeproject.org/metadata/?type=Experiment&accession=ENCSR000ADJ&files.output_category=raw+data&files.output_type=reads&files.status=released"
https://www.encodeproject.org/files/ENCFF001NNN/@@download/ENCFF001NNN.fastq.gz
https://www.encodeproject.org/files/ENCFF001NNP/@@download/ENCFF001NNP.fastq.gz
Brain Control
brain_control.txt
"https://www.encodeproject.org/metadata/?type=Experiment&accession=ENCSR000CDB&files.output_category=raw+data&files.output_type=reads&files.status=released"
https://www.encodeproject.org/files/ENCFF001LAO/@@download/ENCFF001LAO.fastq.gz
https://www.encodeproject.org/files/ENCFF786ODW/@@download/ENCFF786ODW.fastq.gz
xargs -n 1 curl -O -L < brain_control.txt