TOGA

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twobit sizes do not match

10

Hello, I am trying to run TOGA to transfer annotations over from my well-annotated reference to several different query genomes. However, while trying to run TOGA on certain genomes I...

lpnunez

Input file preparation

4

I would like to know how each input file was obtained, and whether I can also use hg38 as a reference genome to apply to other projects. My current understanding...

molinfzl

Question about output alignments

1

Hello! Hope you are all doing well! For the output alignments (nucleotide.fasta, codon.fasta, and protein.fasta), what gene projections/orthology classes are included here? By that I mean, what does TOGA use...

d6948739

Bed file error

13

Hi I am trying to run TOGA, so far u successfully ran the first part to make the alignement. However whenever I try to run TOGA I get an error...

LliliansCalvo

HAL alignments and chaining: post processing TOGA outputs

10

Hi Dr. @MichaelHiller I have couple of queries regarding my TOGA outputs. I am working with vertebrates genomes (size ranging from 550Mb to 1Gb, all genomes that I considered are...

vinitamehlawat

old Java version on run_test.sh micro ValueError: Chain results file TOGA/micro_test_out/temp/chain_results_df.tsv is empty! Abort

22

Not really a bug but using an older version of Java results in the below. Perhaps a more graceful Java version detection and/or warning/error message? Newer Java of course works....

SomePersonSomeWhereInTheWorld

Index error with plot_mutations.py

4

Hello! I am a big fan of this tool, thank you! I want to plot inactivating mutations for various selected transcripts and although I can plot some successfully, others throw...

smorzechowski

TOGA stops after CESAR checking results

2

Hi everyone, I tried to run TOGA using my data and the following command (./toga.py human_mesbid/human.mesbid.final.chain human_mesbid/hg38.wgEncodeGencodeCompV34.bed human_mesbid/hg38.2bit human_mesbid/mesbid.modified.2bit --kt --pn human_mesbid_out -i human_mesbid/hg38.wgEncodeGencodeCompV34.isoforms.txt --u12 human_mesbid/hg38.U12sites.tsv --ms --cjn 32 --cb...

giovannaVeiga

Cache entry deserialization failed, entry ignored

7

Hi Authors, I was able to run TOGA on my couple of species, but somehow, after running for 11 hours, I got this error for one of my species in...

vinitamehlawat

ValueError: invalid literal for int() with base 10: '.'

2

When I run toga.py, it showed up such error info:  Is there anything wrong with my bed file or the python version? Thanks a lot!

YanCheer