Convert Themisto pseudoalignments to kallisto pseudoalignments.
Either use the precompiled binary
or follow the instructions for compiling telescope and libtelescope from source.
- C++11 compliant compiler.
- cmake
- zlib
- Clone the repository, enter the directory and run
> mkdir build
> cd build
> cmake ..
> make
- This will compile the telescope executable in build/bin/ and the libtelescope library in build/lib/.
Convert a single pseudoalignment against 'themisto-index' to kallisto format
telescope --index themisto-index -r pseudos_1.txt -o kallisto_out_folder
... paired-end reads (pseudoaligned separately) considering a read aligned when either of the reads align
telescope --index themisto-index -r pseudos_1.txt,pseudos_2.txt -o kallisto_out_folder --mode union
... considering a read aligned when both of the reads align
telescope --index themisto-index -r pseudos_1.txt,pseudos_2.txt -o kallisto_out_folder --mode intersection
... considering the reads separately (read ids in the second file will be incremented by the number of reads in the first file)
telescope --index themisto-index -r pseudos_1.txt,pseudos_2.txt -o kallisto_out_folder --mode unpaired
... go crazy and do the same with multiple files (the order of the reads must match for the union and intersection options to make sense)
telescope --index themisto-index -r pseudos_1.txt,pseudos_2.txt,pseudos_3.txt,pseudos_4.txt -o kallisto_out_folder --mode union
not yet implemented...
telescope is licensed under the GNU Lesser General Public License v2.1.