TALON

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I was wondering what was your general workflow for working with an expanded annotation from TALON for general differential gene and transcript expression analysis. After generating an expanded annotation working...

callumparr

When running talon with my three samples i get the following error: ``` $ talon --f Analysis/talon/FAT11673.config --db Analysis/talon/WBcel235_gtf_talon.db --build Cel.WBcel235 --threads 12 --o FAT11673 [ 2022-08-19 11:15:36 ] Started...

yeroslaviz

I may overlooked this but I am seeing many TALON novel isoforms that seem illogical short. I was wondering first how this could come to be as the alignment themselves...

callumparr

Optimal setting to identify alternate 3' and 5' ends

3

Hi, I'm interested in identifying alternate 3' and 5' ends of transcripts. What would be the best settings for this? I see the options --5p and --3p in talon_initialize_database, but...

jchariker

Many reads fail QC during TALON run but meet primary, coverage, and identity filters

4

Using TALON v5 installed `python setup.py install` on HPC running Debian Using `python version 3.6.7` ``` talon --f /analysisdata/fantom6/Interactome/ONT-CAGE_TALON_Callum/F6_interactome_config_run2.csv --db /analysisdata/fantom6/Interactome/ONT-CAGE_TALON_Callum/F6_interactome.db --build hg38 --threads 12 --o /analysisdata/fantom6/Interactome/ONT-CAGE_TALON_Callum/F6_interactome_run2 ``` I kept...

callumparr

removing sample(s) from the talon database

8

Hi How does talon process datasets that have only partially been added to the input database? When running talon again using the same config file and input databse will it...

ew367

While running tests on the development branch with these software versions; attrs==21.4.0,iniconfig==1.1.1,numpy==1.22.3,packaging==21.3,pandas==1.4.2,pluggy==1.0.0,py==1.11.0,pybedtools==0.9.0,pyfaidx==0.6.4,pyparsing==3.0.8,pysam==0.15.4,pytest==7.1.1,python-dateutil==2.8.2,pytz==2022.1,six==1.16.0,talon @ file:///woldlab/loxcyc/home/diane/proj/talon/.tox/.tmp/package/1/talon-5.0.zip,tomli==2.0.1 I got this error: ```python test_longest_ends.py:22: _ _ _ _ _ _ _ _ _ _...

detrout

talon says my files dont exist

7

Hi, thanks for making this software available! Any help is appreciated! I call Talon like this: talon --f ./03analysis/talon/TALONconfig.csv \ --db ./03analysis/talon/lr2020talon.db \ --build hg38 -t 8 \ --o lr2020...

abrantesas

ValueError: Annotation name 'aranno' not found in this database. Try one of the following:

1

Hello TALON group, After running your program I get this message: **ValueError: Annotation name 'aranno' not found in this database. Try one of the following:** 'aranno' is the name that...

JD12138

using existing tmp files

2

Hi, I've been having a lot of difficulties running TALON successfully on my very large dataset. After 3 days, I got all tmp files except `abundance_tuples.tsv`. Another whole day passed...

mei-du