TALON

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Issues in identification of genes/isoforms based on the reference GTF in Talon:

3

I used the Talon in Bioconda. I ran the Talon using blank GTF as reference for de novo genes identification. It was successful. However, when I used the output of...

aramaiah

Hey, when I try to run talon_abundance I keep getting this error: > `talon_abundance` --db talon_AF9KO_r2.db.db -a annotation_mm10 --build mm10 --o AF9KO_abundance Warning: Could not locate novelty type for gene...

asipal

What is the meaning of ISM None

2

Hi, I see quite a few models in my TALON output where the transcript novelty assignment is ISM, and the incomplete splice match type is "None". I understand what the...

kathryncrouch

Issue with talon filter

4

Hi, I have been trying to run talon filter on my database: ```talon_filter_transcripts --db talon/database.db -a Hg38 --maxFracA 0.5 --minCount 1 --minDatasets 3 --o talon/talon_run.csv``` And I'm getting an import...

rugilemat

Problem with talon_initialize_database

13

Tried to run talon_initialize_database but got an error: ``` talon_initialize_database --f reference/GRCh38_GENCODE_rmsk_TE_reformatted.gtf \ --g hg38_rmsk_ucsd \ --a hg38 \ --o hg38 chrY bulk update genes... bulk update gene_annotations... Traceback (most...

Kiliankleemann

Thank you to the authors for their work on this tool. I found a workaround that allows the multiprocessing as written to work on Python versions later than 3.7. By...

MLKaufman

When aligning reads with pbmm2 the CIGAR strings use 'X' and '=' instead of 'M'. This causes issues with the `split_cigar` function in `transcript_utils.py`. I am trying the following patch...

ddpinto

Rules for considering splicing variants as identical in TALON

2

Hi, I would like to know the detailed rules when splicing variants are determined to be identical in TALON. If there are multiple isoforms and the start and end points...

mihshimada

Error: value too large to convert to int16_t

1

Hi, I have run talon successfully on a human single cell dataset - thanks for the great pipeline! As part of that experiment we also have a chimp sample. I...

catsargent

Hi there, Just letting you know that I got the following error when running talon. Downgrading numpy to

catsargent