SoloTE v1.09 -- 09/13/2023

SoloTE v1.09 -- 09/13/2023

MAJOR CHANGES / Changes in behaviour

• SoloTE now generates 5 output matrices:

classtes_MATRIX: Results summarized at the class (LTR, LINE, SINE, DNA, RC) level.
familytes_MATRIX: Results summarized at the family level.
subfamilytes_MATRIX: Results summarized at the subfamily level (similar to scTE results).
locustes_MATRIX: Results summarized at the locus level. Only uniquely mapped reads are considered here.
legacytes_MATRIX: Results summarized at the locus level for uniquely mapped reads, and at the subfamily level for multi-mapped reads. This was the default output until v1.08, and the one used in the publication.

• Performance improvements

Code has been cleaned by taking advantage of the versatile options available in SAMtools for BAM processing and filtering.
In turn, the number of I/O operations have been reduced, diminishing the size occupied by temporary files, and speeding up the pipeline.

• Input TE BED file generation

A helper utility, SoloTE_RepeatMasker_to_BED.py, is now packed to allow for a streamlined generation of the Transposable Element BED file required by SoloTE.
For example, for Human hg38, the following command can be run:
python SoloTE_RepeatMasker_to_BED.py -g hg38

This will generate the BED file hg38_rmsk.bed:

chr1    11505   11675   chr1|11505|11675|L1MC5a:L1:LINE|25.1|-  25.1    -
chr1    11678   11780   chr1|11678|11780|MER5B:hAT-Charlie:DNA|29.4|-   29.4    -
chr1    15265   15355   chr1|15265|15355|MIR3:MIR:SINE|23.0|-   23.0    -
chr1    18907   19048   chr1|18907|19048|L2a:L2:LINE|33.8|+     33.8    +
chr1    19972   20405   chr1|19972|20405|L3:CR1:LINE|31.2|+     31.2    + 

Minor changes
Added --minoverlap command line argument. This parameter defines the minimum number of base pairs to annotate a read to a TE (Default = 1 bp).

Bug fixes

• Issues #14, #17: Long-standing matrix generation issues, arising in different systems (i.e., one implementation would work in OSX and not Linux) are now being handled in a platform-independent manner.

SoloTE v1.08 -- 04/14/2023

Bug fixes

• Fixed a bug that resulted in the generation of an improper header of the matrix files in some operating systems.

SoloTE v1.07 -- 04/10/2023

Bug fixes

• "Dual" option was missing from the previous release.

SoloTE v1.06 -- 04/02/2023

Bug fixes

• Fixed an issue causing multiprocessing to not work correctly on Mac OS X computers.

SoloTE v1.05 -- 02/10/2023

Bug fixes

• Issues #6 and #9: Fixed assessment of the tool used to generate the BAM file, at the beginning of the pipeline. Some BAM files generated with CellRanger were not processed correctly.
• Issue #11: Added a line to allow proper detection of the path to the TE BED file.

SoloTE v1.04 -- 01/04/2023

SoloTE v1.04 -- 01/04/2023

Bug fixes

• Issue #7: fixed a bug in the generation of the count matrix.

SoloTE v1.03 -- 12/19/2022

Changes in behaviour
Modified command line arguments. Now each argument can be indicated with flags, as follows:
--threads: Number of threads to use
--bam: BAM file
--teannotation: TE annotation in BED format
--outputprefix: Output files prefix
--outputdir: Output directory (if it doesn't exist, it will be created)

SoloTE can be executed in this manner:
python SoloTE_pipeline.py --threads NumberOfThreads --bam BAMfile --teannotation BEDfile --outputprefix Prefix --outputdir OutputDirectory

Bug fixes

• Issue #6: fixed the issue that stopped SoloTE to continue with CellRanger BAM files.

SoloTE v1.02 -- 10/26/2022

Changes in behaviour
Modified command line arguments. Now each argument is as follows:

1. BAM file
2. Threads
3. Output directory
4. TE annotation in BED format
5. Output prefix

In order to run SoloTE, the command should be provided in this way:
python SoloTE_pipeline.py BAMfile Threads OutputDir TEannotationBEDfile OutputPrefix

Bug fixes

• Issues #2, #3: fixed the issue that caused SoloTE to crash when using BAM files that have the GN:- tag for not genic reads.
• Fixed an issue related to paths created during SoloTE execution.