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operating system : Ubuntu Server 24.04 LTS
all dependencies for SYNY are already installed
shell command:
ka@prot:~$ /data2TB/apps/SYNY/Utils/gff3_to_gbff.pl -f $HOME/Documents/Tricho/syri/Tatrov…
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Hello,
I am trying to prepare a data file for visualization using this software, but I don't understand what the score values in the 4th column of your example file (rice_MH63_repeat.bed) mean, as…
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Hi! I am not sure if this is a question for nextclade or augur.
I am using `augur ancestral` as part of a pipeline to create a tree for use in a nextclade dataset: https://github.com/anna-parker/ma…
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Hi,
I am trying to generate sashimi plots using BAM files made from running rMATS on FASTQ files. I am using two files that hold my replicates.
My run:
python /Packages/rmats2sashimiplot/src/rm…
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**Describe the bug**
I lifted annotations from a reference genome to another isolate with LiftOff. I wanted to check how the new annotations are. Do they have start and stop codons or in-frame/premat…
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Hello gggenomes folks.
I am currently attempting to run your program on my dataset that are subsections of:
1. A Nucleotide Fasta file- a portion of my chromosome JAEVHH010000002.1 from length 609…
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In bacterial genomics we normally want the annotations *and* the sequences/contigs. This tool currently only handles each separately (as that is how NCBI provides it) via `-F fasta` and `-F gff3`.
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Hello!
I have got a de novo genome assembly from Illumina PE sequencing. This assembly has got 8.7 million scaffolds in fasta format. I splitted this fasta file to multiple fasta files. One fasta f…
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Hi Brian,
I followed the steps, but failed at the final step:
`~/miniconda3/opt/transdecoder/util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 transcripts.gff3 transcript…
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Dear the authors:
Thanks for devoloping such an useful program. Now I have a question that if I have mutiple GFF3 files to train bssm, how can I merge these files for the gthbssmtrain program? I do n…