Tobias Jakobi
Tobias Jakobi
Using `bedtools map` I get this strange error that is different from the results with previous bedtools versions (i.e. 2.28.0): ``` tjakobi@t470-tjakobi> bedtools --version bedtools v2.30.0 tjakobi@t470-tjakobi> bedtools map -c...
I am trying to run the second part of the analysis based on StringTie data on an improved genome annotation based on an initial Ensembl genome. With the default Ensembl...
A module to design siRNA sequences for use with circlular RNA was suggest on the SPP1738 conference and seems like a natural extension of circtools' functionality.
Right now the Excel file could provide more detailed information that is scattered throughout different files. This information should be unified in the produced .XLS file. Bonus points: can we...
Those events can be found in the data files and are plotted. However, what does it mean? The BSJ is neither covered by one nor by two mates, so how...
Currently visualization is done using raw `#circRNA isoforms/gene` counts. It would be more helpful to normalize the count in a RPKM/FPKM like manner, e.g. `isorms per kilobase `.
We need to revisit the topic of macOS portability. First tests show a more or less straightforward way to get the installation with dependencies going. However, execution of the modules...
We require a module that is able to asses / analyse the conservation on gene as well as back splice junction level across different species.
Benchmarks shows that the IO-heavy work flow of bedtools has a severe impact of the performance. It would be reasonable to instead use Brandon's replacement functions.
Support for zipped files is de-facto standard and would also help reduce disk space used.