Moderator: Daniel Standage

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Daniel Standage3.7k
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Location:
Davis, California, USA
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http://standage.github...
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byuhobbes
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Husband, father, scholar, aspiring scientist, avid programmer, lapsed musician, flipper of pancakes, baker of biscuits.

Posts by Daniel Standage

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Comment: C: Warning message: [outdir] is not a file, ignoring
... Yeah, I was afraid this might be the "correct" answer. Indeed, the contigs are the primary interest of output. But in cases where an assembler performs strangely it's useful to have all of the other ancillary and intermediate files around as well for troubleshooting. Declaring each of these files ex ...
written 12 months ago by Daniel Standage3.7k
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Warning message: [outdir] is not a file, ignoring
... I am familiarizing myself with Docker, Common Workflow Language, and Dockstore. I've created a simple wrapper for the MEGAHIT assembler, and followed Dockstore's instructions for building a Docker image, describing the tool in CWL, and specifying inputs and outputs with JSON. Here is the tool descr ...
dockstore cwl written 13 months ago by Daniel Standage3.7k • updated 12 months ago by Michael R. Crusoe1.0k
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Answer: A: Genome annotation using EST assembly
... [PASA][1] was one of the first, if not the first, EST assembly programs that existed long before RNA-Seq was in vogue. You splice-align transcripts using a program like [GeneSeqer][2], and then PASA assembles the alignments. I haven't personally used it for annotation, but in its documentation PASA ...
written 20 months ago by Daniel Standage3.7k
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Comment: C: gff3 to CDS fasta
... I'm not sure I understand your constraints. If you are uncomfortable evaluating custom Perl/Python scripts and if installing new software is impractical for you, you may be in the wrong field! I'm not trying to be witty or smug, I'm being completely frank. The bioinformatics state of the art unfort ...
written 20 months ago by Daniel Standage3.7k
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Answer: A: gff3 to CDS fasta
... The `xtractore` program from the [AEGeAn Toolkit][1] should work for this. Set `--type=CDS` on the command line. For CDSs and other discontiguous features, `xtractore` pastes the fragments together correctly, taking into account strand, etc. [1]: http://brendelgroup.github.io/AEGeAn/ ...
written 20 months ago by Daniel Standage3.7k
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Answer: A: GFF3 ID field: "Official" nomenclature
... Michael's answer is excellent. I want to reiterate a few of his points before I add another of my own. - **exons appearing in multiple isoforms**: In the "canonical gene" shown in the official [GFF3 specification](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) (recentl ...
written 23 months ago by Daniel Standage3.7k
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Answer: A: How to convert a gff3 to gtf?
... I've been able to find GFF3 to GTF converters (as well as GTF to GFF3 converters) before with some Googling. My go-to is the **gt gff3_to_gtf** program distributed with [GenomeTools](http://genometools.org). However, I think it's important to state that any converter between GTF and GFF3 will neces ...
written 23 months ago by Daniel Standage3.7k
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Answer: A: infer 3' and 5' UTR from gff3 file
... The **canon-gff3** tool from the [AEGeAn Toolkit](http://brendelgroup.github.io/AEGeAn/) will infer UTRs (and start/stop codons) from gene structures such as those you describe. ...
written 23 months ago by Daniel Standage3.7k
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Encoding zero-length features in BED format
... What is the convention for encoding zero-length features (that is, features between two nucleotides) in BED format? Would I use [0, 0) or [1, 1) to describe the site between the 0th base and 1st base? ...
genome bed coordinates written 2.4 years ago by Daniel Standage3.7k • updated 2.4 years ago by Chris Miller20k
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Comment: C: How to group features based on ID in gff
... I've seen a few different conventions for encoding alignments in GFF3. The first example you gave is perfectly valid (as far as the GFF3 specification is concerned: individual tools may have specific requirements). sequence source EST_match 1 20 . - . ID=ID1; sequence source EST_match ...
written 2.7 years ago by Daniel Standage3.7k

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