Moderator: Daniel Standage
Daniel Standage ♦ 3.9k
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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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... 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 3.3 years ago by
Daniel Standage ♦ 3.9k
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... 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 ...
written 3.3 years ago by
Daniel Standage ♦ 3.9k
• updated
3.3 years ago by
Michael R. Crusoe • 1.8k
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... [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 4.0 years ago by
Daniel Standage ♦ 3.9k
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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 4.0 years ago by
Daniel Standage ♦ 3.9k
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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 4.0 years ago by
Daniel Standage ♦ 3.9k
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... 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 4.2 years ago by
Daniel Standage ♦ 3.9k
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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 4.2 years ago by
Daniel Standage ♦ 3.9k
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... 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 4.2 years ago by
Daniel Standage ♦ 3.9k
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... 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?
...
written 4.7 years ago by
Daniel Standage ♦ 3.9k
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4.7 years ago by
Chris Miller ♦ 21k
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... 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 5.0 years ago by
Daniel Standage ♦ 3.9k
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