TEspeX_v_2.0.1

released on 18/11/2022

• TEspeX now checks that no redundant sequence headers are found among the three input fasta files. If found, an error is rose and the run is killed

Thanks to Davide Bressan (University of Trento, ITA) | (https://github.com/DavideBrex) for reporting the bug.

TEspeX_v_1.2.1

Released on 06.07.2022

• fixed minor issues

TEspeX_v_1.2.0

Released on 07.06.2022

• New --multimap parameter has been added to this new TEspeX version. Through this parameter the user can now define the maximum number of multiple loci a read/read pair can align to. The default value is 10 and we recommend not to change this. The provided number will be passed to STAR --outFilterMultimapNmax and --winAnchorMultimapNmax parameters. So, if you really want to change them, please, carefully read the STAR manual before doing that

TEspeX_v_1.1.1

• the --module parameter has been added to TEspeX wrapper. Sometimes it might be that while running TEspeX, some installed modules need to be uploaded in the running environment. If this is the case, provide the list of modules through this parameter. TEspeX will then take care of uploading the listed modules in each job by module load <module name>
• until TEspeX v 1.1.0, TEspeX could be run in wrapper mode on SLURM systems only. Here, wrapper_pbs.py is provided and should IN THEORY work on PBS-based systems. This, however, has not been extensively tested

TEspeX_v_1.1.0

Released on Oct 8th 2021

• Fixed minor bug in counting reads, TE counts from this version might slightly differ from the previous versions one if the reads have been trimmed before launching TEspeX

TEspeX_v_1.0.4

Released on 24.08.2021

• added the --mask parameter
• STAR is now provided as executable - no need to download it anymore

TEspeX_v_1.0.3

TEspeX v1.0.3 - 29.07.21

• installation of conda and other required tools is now step-by-step explained in the README
• fixed the code such as only the python libraries installed within the TEspeX_deps environement are used. This grants that TEspeX uses exclusively the newly installed python libraries resolving potential conflicts with previously installed python libraries

TEspeX_v_1.0.1

Released on 20th Jul 2021.

• to simplify the installation of TEspeX, the installation now occurs through a conda environment. The user is therefore required to have conda installed and in $PATH. Through conda a TEspeX_deps environment based on python 3.6 is created. Then, within the environment, the required versions of pysam and pandas are installed.
• this allows more installation flexibility and, most importantly, does not interfere with previous/future installation of pandas and pysam
• STAR and samtools are installed as in the previous releases
• updated the installation manual accordingly

TEspeX_v_1.0

This is the release 1.0 of TEspeX.

• Additional checks on the arguments provided by the user have been added
• The pipeline checks the required versions of the pandas libraries are installed
• --q and --walltime are added to the wrapper script in order to simplify the job-launching operations

TEspeX_v_0.2.1

First release of TEspeX