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Issues list

Do you recommend to improve the annotation of an existing genome with TOGA?
#188 by MauriAndresMU1313 was closed Oct 29, 2024
5
Test-data does not pass the step 2 and environment does not detect some libraries
#187 by MauriAndresMU1313 was closed Oct 29, 2024
9
Error with CESAR_wrapper.py: realign_exon _ ValueError: too many values to unpack
#185 by vpymerel was closed Sep 29, 2024
2
Post-TOGA queries related to UL (Uncertain loss) and L (loss) status
#183 by vinitamehlawat was closed Oct 31, 2024
2
The certainty of uncertain states in TOGA
#181 by molinfzlvvv was closed Oct 31, 2024
5
Exon related statistics
#180 by wang748 was closed Aug 23, 2024
3
TOGA as a tool to age genes?
#179 by DiegoSafian was closed Oct 31, 2024
3
Treatment of different gene sets
#178 by molinfzlvvv was closed Aug 22, 2024
1
Script to convert gtf file to TOGA input
#177 by DustinSokolowski was closed Aug 19, 2024
1
how to interpret the output plot
#176 by aaannaw was closed Oct 31, 2024
6
support for transferring miRNA annotations?
#173 by lichennan123 was closed Oct 31, 2024
4
run with multiple query genomes
#172 by philge was closed Oct 31, 2024
1
The different results of the same gene in two assemblies
#171 by txfc was closed Jul 11, 2024
4
Questions about the outputs of TOGA "loss_summ_data.tsv" and "proteinAlignments.fa"
#170 by SWei2333 was closed Oct 31, 2024
1
TOGA annotation of sex chromosomes
#167 by smorzechowski was closed Jun 10, 2024
2
Operational problems with CESAR2.0
#165 by molinfzlvvv was closed Jun 5, 2024
1
The question of inactivate mutation identification
#163 by txfc was closed Jun 14, 2024
3
Output file interpretation
#162 by molinfzlvvv was closed Oct 31, 2024
1
Assembly_stats:KeyError: "None of [Index(['vs_/home/vlamba/1March-Query4-gene-loss/'], dtype='object')] are in the [index]"
#155 by vinitamehlawat was closed Apr 26, 2024
9
Some genes lost in the loss_summ_data.tsv
#154 by txfc was closed Apr 18, 2024
7
Non-unique transcript names assigned to invalid chain IDs
#153 by ning-y was closed Apr 10, 2024
4
ValueError: Chain results file chain_results_df.tsv is empty! Abort.
#152 by txfc was closed Apr 3, 2024
6
Questions about custom training of XGBoost models
#149 by fuesseler was closed Mar 1, 2024
4
duplicate transcript names in query_annotation.bed
#147 by fuesseler was closed Feb 19, 2024
4
Re-run CESAR jobs crash- "some para/nextflow processes died"
#146 by pfb2201 was closed Feb 26, 2024
10
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