Finder

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Final output annotation

1

Hi @sagnikbanerjee15 Finder is a pretty useful program. Can you please add --keep-gene-names in when running gffread? Otherwise, annotations of genes are missing. Thanks

ZuyaoLiu

Use of Long Read (PacBio IsoSeq)

1

May I ask if FINDER is compatible with long read sequencing? If not, how do you recommend enhancing the annotation results with the FINDER output using such data? Thanks a...

saxovocal

Protein FASTA from closely related species

1

Thank you for the wonderful package. I have plenty of transcriptome data for my species, but I do not have a protein fasta. Is it recommended to use a protein...

saxovocal

Issue during Braker

2

It seems finder is failing during braker and I can't quite determine why. Attatched is the progress log, the error file, and the job script I used. I emailed the...

ombarr

Installation: error, required file not found: hmm_to_gtf.pl

3

When running ./install.py, I receive this error after following the installation instructions. The solution seems to just be copying and pasting "hmm_to_gtf.pl" from the "other" directory within "gmes_linux_64" to the...

chutter

Finder on local data

3

Hello there, Thank you for a wonderful software. I am trying to use finder with RNAseq data which resides on my local machine. From the logs it seems that its...

utritala

SRA download as fastq.gz

1

Hello Would it be possible that the downloading process generate fastq.gz files instead of fastq ? I know that there is an option that can delete later those files but...

blavetn

Trouble running the example

56

Hi, and congratulations for the software. I want to give a try, and I managed to successfully install it (the conda environment and the step-by-step process is much appreciated, but...

josruirod

Overloading and High memory consumption while downloading data

4

Hi there, thanks for developing `finder` I am currently running `finder` on a fungus genome. I put several dozens of SRA libraries in the metadata file. The process is currently...

sivico26

IndexError

5

Hi there. I've been having issues running both the example and on my own data, see below: `~/finder/finder -no_cleanup -mf ~/finder/example/Arabidopsis_thaliana_metadata.csv -n 6 -gdir_star /Volumes/TOSH_EXTERNAL/star_index_without_transcriptome_Arabid -out_dir /Volumes/TOSH_EXTERNAL/Finder_Output1 -g ~/finder/example/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa -p...

nick294