Finder

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Wrong XA format and combined/psiclass_output_vote.gtf': No such file or directory

1

Hello there Thanks for having developed this tool I'm having the same problem as many but I cannot solve it (I already put this message at the end of an...

Dalhte

Mapping rate in round 2 0.0

9

I'm having an issue with the pipeline that I can't quite narrow down. Here's what's printed to the screen: `wirenia@wirenia:~/Desktop/2021-04-21_Hanleya_finder$ ./run_finder.sh cat: output/alignments/Hanleya_hanleyi_mantle_round1_SJ.out.tab: No such file or directory cat: output/alignments/Hanleya_hanleyi_mantle_round2_SJ.out.tab:...

kmkocot

example output files

1

Hello, I was wondering if you could make available on GitHub the GTF files generated by Finder when run on the "example" dataset? Both the "final_GTF_files/ *.gtf" and "assemblies_psiclass_modified/*gtf" files...

dpuiu0

Finder does not find files (supposed to be) generated at earlier steps...

5

We are running finder at the command line. Now we know that the "Required parameters" as in the help file, and if provided in an empty directory do not work,...

lefterov

Finder on PacBio data

3

Hello, I am currently trying to run finder on three whole genome samples: 1. Sequenced with Illumina HiSeq x ten 2. Sequenced with Illumina Novaseq 6000 3. Sequenced with PacBio...

WietseHR

Unable to find combined.gtf file

2

Hi, I'm trying to run FINDER for a Hawaiian Drosophila genome. However, I got this problem: " FileNotFoundError: [Errno 2] No such file or directory: '/storage/pricelab/ngoc/Finder-finder_v1.1.0/silvestris/assemblies_psiclass_modified/combined/combined.gtf' Please let me know...

bimbim1803

Issue running Finder

5

Hello, bellow i post the output of the run with finder pipeline. It looks like some alignment files that should be produced by Finder are not produced, STAR aligner is...

nousiaso

codan fails and kills pipeline due to finding duplicate key(s)

4

Running the latest run_finder-v1.1.0. Everything runs fine until the codan step (Braker is complete), which finds a duplicate key and kills the pipeline. Looking at the assemblies_psiclass_modified/combined/combined_split_transcripts_with_bad_SJ_redundancy_removed.fasta file for duplicated...

laurabaxter21

error with example file

1

Thank you for making your software available. I have tried to run the example script. I am using an M1 Mac OS 13.2.1. When I run theoneal@MacBook-Pro ~/Finder-finder_v1.1.0 $ run_finder...

theokirkland

metadata file and soft masking

5

Could you please explain how to prepare metadata file and which tool is suggested for soft masking of the genome?

ardy20