This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Trinotate sqlite and gene_to_trans_map

Hi, I would like to run autoTrinotate.pl but how do I generate files for parameters --Trinotate_sqlite and --gene_to_trans_map?

Thank you in advance,

rna-seq
• 842 views • link
written by Ric Ric

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Retrieving sequences and Blast them
    written by Ric Ric
    Hi, I would like to use the virus sequences from [here](https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239&host=land+plants) and blast them againt our genome. How is it posssible to download the sequences …
  • issue with autotrinotate.pl
    written by hydra_questions • hydra_questions
    Hi! I keep getting the error below while trying to run the autoTrinotate.pl script for my Trinity-assembled transcriptome (fasta file). Any advice on where the …
  • annotation with Augustus
    written by Ric Ric
    Hi, we have a plant genome and would like to create an annotation with Augustus. However, I am not sure about the following few parameters. …
  • Repeats detection in a genome
    written by Ric Ric
    Hi, I would like to detect repeats in my genome and I did the following steps: > conda activate repeats > BuildDatabase -name Repeats ragoo.fasta …
  • counting the number of reads in FASTQ files
    written by Ric Ric
    Hi, I would like to get the read coverage and I found [here][1] C = LN / G whereas: - C stands for coverage - …
  • Gene clustering with OrthoMCL
    written by Ric Ric
    Hi, I would like to run [OrthoMCL](https://gist.github.com/darencard/59df52f68c9195ea926698131f7f5d3c) and as input, it requires protein sequences from desired organisms. Does OrthoMCL use assembled transcript from RNA-Seq? Thank …
  • Hi-C programs recommandations
    written by Ric Ric
    Hi, I have a plant assembly which has been polished pilon. Next, I would like to use Hi-C to create chromosome bins. Which software would …
  • Removing reads shorter than 10kb from FASTQ files
    written by Ric Ric
    Hi, How is it possible to remove reads shorter than 10kb from FASTQ files. I found how to do it FASTA files but not for …
  • How to find Bloom filter parameter for Abyss 2
    written by Ric Ric
    Hi, Abyss 2 introduces a new Bloom filter assembly mode that enables large genome assemblies with minimal memory. Bloom filter assembly mode is enabled by …
  • removing chloroplast sequence from FASTQ files
    written by Ric Ric
    Hi, I have paired-end WGS FASTQ files and chloroplast genome. How is it possible to remove chloroplast sequences from the FASTQ files? Thank you in …