Step 2: Prepare Sample Data

GEMmaker is capable of processing both locally stored RNA-seq files and automatically downloading samples stored in the NCBI SRA database. You can provide both types of files to be included in a single run of GEMmaker, or use only local or only remote files.

Using Samples From NCBI SRA

GEMmaker supports automatic download and processing of samples from the NCBI SRA repository. To use samples from the SRA, you must first find the list of NCBI SRA Run IDs of the samples you want to process. The run IDs typically start with an SRR, ERR, or DRR prefix. Do not confuse these with the Experiment IDs which typically start with SRX, ERX or DRX. The run IDs must be placed, one per line, in a file.

Example of a remote ID File:


Using Samples Stored Locally

By default, GEMmaker expects that FASTQ files are uncompressed (not GZ compressed). They can be stored in any directory on the local filesystem.

Paired FASTQ files

By default, paired files must have a _1.fastq and a _2.fastq suffix at the end of the filename. GEMmaker uses the _1 and _2 designation to differentiate and match paired files.

Non-Paired FASTQ files

By default, if your data is non-paired, GEMmaker expects all files to have a _1.fastq suffix at the end of the filename.