User: joelepaul

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Posts by joelepaul

<prev • 7 results • page 1 of 1 • next >
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Merge two genome annotation files: one annotated by contig, the other annotated by scaffold.
... Hi @ll! After doing what was recommended to me in my previous post ( https://www.biostars.org/p/446515/ ), I ended up with two annotation files. EVM produced an annotation on a scaffold level ("scaffold1234"), BLAT produced an annotation on the contig level ("RDRX12302"). Now I am wondering how do ...
annotation written 2 days ago by joelepaul0 • updated 2 days ago by lieven.sterck7.9k
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Match predicted sequences to reference genome to generate data for annotation GTF
... Hi @ll! From a paper, I have obtained a list of ~10 predicted sequences for specific proteins (predicted from transcriptomes). Now I would like to match these sequences with the reference genome so as to reveal annotation data (not only "position" but also scaffold ID, score, strand and frame - see ...
annotation written 2 days ago by joelepaul0
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Manually adding genome annotation to annotated file
... Hi @ll! With funannotate I have predicted the annotation for a reference genome of a species that does not have a previous annotation and saved this annotation in a GFF3 file. Now, I have found a recent publication with a functional annotation for 5-10 DNA sequences/proteins of the same species, su ...
annotation written 4 months ago by joelepaul0 • updated 3 months ago by Kevin Blighe61k
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Comment: C: Conversion GFF to GTF for specific non-model genome
... My main issue is that there is no hmm model of a remotely close species to this snail. Gastropods/molluscs are not vertebrates or mammals, not worms, not insects, not plants and not fungi. ...
written 4 months ago by joelepaul0
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Comment: C: Conversion GFF to GTF for specific non-model genome
... That's a bummer. Unfortunately I do not have the funds available to create a real annotation, so I cannot apply the pipeline that I wanted to (which wants a GTF file as a mandatory requirement). Is there maybe a way to "simulate" an annotation without actual work on the DNA, such as described here: ...
written 4 months ago by joelepaul0
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Conversion GFF to GTF for specific non-model genome
... Hi @ll! I am working with a recently sequenced genome of a non-model system, which is this one: https://www.ncbi.nlm.nih.gov/assembly/GCA_004329575.1/ The assembly that I can download from there includes only a *.GFF file. A *.GTF file is available too, but it is largely empty (the GFF is not). M ...
gtf gff written 4 months ago by joelepaul0 • updated 4 months ago by Juke344.3k
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bamtools filtering syntax - reads containing more than X mismatches and soft-clipped reads
... Hi @ll! I'm extremely new to the field of bioinformatics, though I have some programming knowledge. A lot of tools have quite nice manuals out there, which helps me learning about how to use them properly. However, when it came to bamtools, I have been stuck. My aims are twofold - starting from ni ...
bwa bamtools written 4 months ago by joelepaul0 • updated 4 months ago by Pierre Lindenbaum129k

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