11 Issues closed by 3 people

• The number of genes annotated is low

  #52 closed Nov 4, 2024

• Output file interpretation

  #162 closed Oct 31, 2024

• Questions about the outputs of TOGA "loss_summ_data.tsv" and "proteinAlignments.fa"

  #170 closed Oct 31, 2024

• run with multiple query genomes

  #172 closed Oct 31, 2024

• how to interpret the output plot

  #176 closed Oct 31, 2024

• support for transferring miRNA annotations?

  #173 closed Oct 31, 2024

• TOGA as a tool to age genes?

  #179 closed Oct 31, 2024

• Post-TOGA queries related to UL (Uncertain loss) and L (loss) status

  #183 closed Oct 31, 2024

• The certainty of uncertain states in TOGA

  #181 closed Oct 31, 2024

• Test-data does not pass the step 2 and environment does not detect some libraries

  #187 closed Oct 29, 2024

• Do you recommend to improve the annotation of an existing genome with TOGA?

  #188 closed Oct 29, 2024

2 Issues opened by 2 people

• Getting 5' UTR of a gene from TOGA orthologs

  #189 opened Nov 3, 2024

• how to set paramenters without cluster?

  #186 opened Oct 15, 2024

3 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• Could not split CESAR jobs

  #121 commented on Oct 25, 2024 • 0 new comments

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

  #131 commented on Oct 28, 2024 • 0 new comments

• CDS length not divisible 3

  #182 commented on Oct 31, 2024 • 0 new comments