CREMA - How to submit data

How to submit your data.

Data can be uploaded either through the CREMA website , or by using the CREMA uploader python script.

There are two possible ways to submit the data to CREMA:

Upload files from your own computer.
Provide a list of URL links to the data files.
Provide a list of SRR IDs.

Uploading files on the website.

First provide your email address and a name for your project. CREMA will notify you via email when its analysis of your data is ready, and use the project name for reference.
Select your data type, i.e. whether you have DNA accessibility (ATAC/DNase-Seq) or enhancer marks (ChIP-Seq) data.
Select the appropriate organism/assembly version.
Click the "add files" button and select all the files you want to upload. Note you can click the button multiple times.
Your file set should include FASTQ files and samples.tsv file with meta information about the FASTQ files (see below).
Click the "Start upload" button.

Submit a list of links.

First make sure you provided a contact email and selected the correct data type and organism/genome assembly.
Click the "add files" button and upload samples.tsv file which contains links to the fastq files and corresponding meta information. (See description of samples.tsv file.)
Click the "Start upload" button.

Submit a list of SRR IDs.

First make sure you provided a contact email and selected the correct data type and organism/genome assembly.
Click the "add files" button and upload samples.tsv file which contains SRR Ids and corresponding meta information. (See description of samples.tsv file.)
Click the "Start upload" button.

Samples.tsv file format.

This file contains description of your data that is a sample name, type and corresponding files (or/and links, SRR IDs). File should be in TSV (tab separated values) format.

There are four columns:

sample name - a comprehensive sample name.
sample type - a type of a sample, which is either fg for ChIP-seq IP samples and DNA accessibility samples, or bg for input ChIP-seq samples.
File name of the sample FASTQ file, or a link to the sample FASTQ file, or corresponding SRR ID.
In case of paired end FASTQ files, the fourth column contains file name of the second end FASTQ file, or an URL of the second end FASTQ file. If your data is single end, then leave this column empty.

Example samples.tsv with files:

sample	        type	fq1	                fq2
condition1	fg	file1.fastq.gz
condition1	bg	file2.fastq.gz
condition2	fg      file3_R1.fastq.gz	file3_R2.fastq.gz
condition2      bg	file4.1.fastq.gz	file4.2.fastq.gz

Example samples.tsv with links:

sample	        type	fq1	                                fq2
condition1	fg	ftp://myftp.org/file1.fastq.gz
condition1	bg	ftp://myftp.org/file2.fastq.gz
condition2	fg      https://myhost.org/file3_R1.fastq.gz	https://myhost.org/file3_R2.fastq.gz
condition2      bg	https://myhost.org/file4.1.fastq.gz	https://myhost.org/file4.2.fastq.gz

Example samples.tsv with SRR IDs:

sample	        type	fq1	                                fq2
condition1	fg	SRR3452187
condition1	bg	SRR3452188
condition2	fg      SRR3452189
condition2      bg	SRR3452190

CREMA Cis-Regulatory Element Motif Activities