Finder

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Genome examples empty?

18

Hi I am trying to predict gene structure using Finder. And it seems this tool is better than PASA, MAKER,,, So I am planning to get used to this tool....

paul-bio

Output files not always containing CDS filed

3

Hello, I was checking the output files because I want to generate a protein fasta in order to run BUSCO. I realized that some files like "combined_with_CDS_high_and_low_confidence_merged.gtf" contain a CDS...

vccarneiro

cds_predict error

5

Hello there, I'm trying to use FINDER for the first time, on a Drosophila de novo assembly with locally stored RNA-seq data. Many parts of the pipeline seem to have...

claumer

dummy_data file issue - Singularity

7

Hi! I'm trying to run the example data (testrun) in Finder on an HPC using Singularity (v 3.7.1). In the main testrun.error file the error that starts the error series...

njm-data

Low BUSCO stats

2

Hi! My previous annotation with MAKER and BRAKER had ~97% complete BUSCO genes for the genome I have. This was consistent with outputs from BUSCO directly run on the genome....

skyungyong

Finder failed to analy

10

Hi Sagnik I'm trying to run finder on the provided example data. However, it's just failing and trowing the following error. Any help is appreciated. finder -no_cleanup -mf test_metadata.csv -n...

jb018

Why the busco scores for the annotated example arabidopsis thaliana genome proteins are very low ?

3

Dear the authors, Thanks a lot for your valuable and user-friendly software. I have tried the finder programe to annotate the example arabidopsis thaliana genome, but found the proteins extrated...

bioinformaticspcj

Error: "finder: Argument list too long"

12

Dear Sagnik, I am trying out the example data and wondering what argument could be causing this error and how do I fix it! # finder -no_cleanup -mf Arabidopsis_thaliana_metadata.csv -n...

vccarneiro

Will this error affect final results?

1

Hi, I got the following error when running finder, will it affect the final results? fixOverlappingAndMergedTranscripts.py:347: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or...

xiekunwhy

Final output has many gene annotations in repetitive regions

9

@sagnikbanerjee15 I found that in the final output, many genes are located in repeat regions. It seems the soft masking of the genome doesn't work well. Got any idea? Thanks

ZuyaoLiu