Please refer to the documentation for more in depth details.
Berg JA, et. al. (2019). XPRESSyourself: Enhancing and Automating the Ribosome
Profiling and RNA-Seq Analysis Toolkit. https://github.com/XPRESSyourself.
The following is a short tutorial showing you how to install XPRESSpipe:
- Make sure you let Anaconda set up the PATH info for you.
- If the help menu is not displayed when testing, try adding the path where you installed XPRESSpipe to the system PATH
$ echo 'export PATH=$PATH:/path/to/xpresspipe' >> ~/.bash_profile
If you do not have a file names ~/.bash_profile, try looking for one called ~/.profile
-
Reference building
-
Running XPRESSpipe on sequence data
-
You can also use the XPRESSpipe command builder and executor for reference curation or running the pipeline by executing the following:
$ xpresspipe build
inputdirectory with raw sequence data- Sequence data files should be
FASTQformat and end in.fastqor.fqand can be.zipor.gzcompressed
- Sequence data files should be
- An empty
outputdirectory - A
referencedirectory (see documentation forcurateReferencefor more details)
In order for ordered output after alignment (except for generation of a raw counts table), recommended file naming conventions should be followed.
- Download your raw sequence data and place in a folder -- this folder should contain all the sequence data and nothing else.
- Make sure files follow a pattern naming scheme. For example, if you had 3 genetic backgrounds of ribosome profiling data, the naming scheme would go as follows:
ExperimentName_BackgroundA_FP.fastq(.qz)
ExperimentName_BackgroundA_RNA.fastq(.qz)
ExperimentName_BackgroundB_FP.fastq(.qz)
ExperimentName_BackgroundB_RNA.fastq(.qz)
ExperimentName_BackgroundC_FP.fastq(.qz)
ExperimentName_BackgroundC_RNA.fastq(.qz)
- If the sample names are replicates, their sample number needs to be indicated.
- If you want the final count table to be in a particular order and the samples ordered that way are not alphabetically, append a letter in front of the sample name to force this ordering.
ExperimentName_a_WT.fastq(.qz)
ExperimentName_a_WT.fastq(.qz)
ExperimentName_b_exType.fastq(.qz)
ExperimentName_b_exType.fastq(.qz)
- If you have replicates:
ExperimentName_a_WT_1.fastq(.qz)
ExperimentName_a_WT_1.fastq(.qz)
ExperimentName_a_WT_2.fastq(.qz)
ExperimentName_a_WT_2.fastq(.qz)
ExperimentName_b_exType_1.fastq(.qz)
ExperimentName_b_exType_1.fastq(.qz)
ExperimentName_b_exType_2.fastq(.qz)
ExperimentName_b_exType_2.fastq(.qz)