8 votes
Accepted

How GFF3 attributes (9th column) varies from one gene prediction algorithm to another

The first place to start is the GFF3 specification. This is the official word on what is and is not allowed in a GFF3 file. For example, users can define arbitrary attribute keys, so long as they do ...
user avatar
5 votes
Accepted

Software recommendation: find DNA sequence distribution over entire transcript

If I understand the question correctly, you'd like to plot the positions of the matches to you motif along with a gene model that shows the positions of introns and exons for the different transcripts....
user avatar
  • 1,806
4 votes

Annotation format design

I quite like BED and GFF3 (I don't like GTF/GFF2, though). As text-based formats, I don't think they leave us much room for improvement. Anyway, if you want a new format, here is one. The following is ...
user avatar
  • 5,645
4 votes

Annotation format design

The problem is that GFF, fundamentally, is a relational format: it provides tags that relate individual rows via one-to-many relationships (e.g. gene–exon). This indirectly highlights the second ...
user avatar
4 votes

Annotation format design

Presuming we consider "human readable", "easily parsable", and "quickly queryable" to be objectively good qualities (and if not, I worry for the future): Text-based: It's absurdly common to want to ...
user avatar
  • 19.3k
4 votes

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

The three # are used for splitting group of features that belong together, e.g. a transcript and it's exons. Sometimes you see with a blank line instead of the <...
user avatar
  • 1,322
4 votes
Accepted

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

There are some good answers so far, but I don't think any of them fully communicate the significance of the ### directive. The GFF3 specification states: This ...
user avatar
3 votes
Accepted

What is the `table` parameter in the UCSU ldHgGene tool?

I stumbled across this issue after getting the same warning message from liftOver. By using the -out option of ...
user avatar
  • 46
3 votes
Accepted

Problem installing RATT

Usually the home of a program is where the executable is. In order to make the system aware you need to include it as a variable when the terminal is run. So you need to add it to the file at ...
user avatar
  • 4,622
3 votes

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

As others have stated, those are just there to separate the entries for easier parsing. They enable you to do nifty tricks like: ...
user avatar
  • 7,957
3 votes
Accepted

COG Annotation - Dealing with genes assigned to two or more COG categories

You add 1 to the count of each COG category. You are looking for over represented COG categories so you must count them all. Many genes will be assigned to multiple categories. In fact, a majority of ...
user avatar
  • 7,957
3 votes

seqret error when trying to transform GFF3 and FASTA files into EMBL format

I'm one of the EMBLmyGFF3 developers. If the compressed annotation is 396MB as mentioned by @terdon it is not a small annotation... In the worse case we have tested we never waited more than few ...
user avatar
  • 141
2 votes
Accepted

seqret error when trying to transform GFF3 and FASTA files into EMBL format

That error is telling you that the script you were running was killed by signal 9, also known as SIGKILL, while executing the ...
user avatar
  • 7,957
2 votes

Is there any tools that can generating FBA model from genome sequences or proteome sequences?

To generate flux balance, one should now the stoichiometric numbers of all the reactions that are taking place, as well as the conditions (that could affect the reactions). I am not sure we have ...
user avatar
  • 4,622
2 votes
Accepted

Accessing UCSC genome via ssh results in a validation error

You need to setup ssh keys. All the commands in the script are going to use ssh to run the commands. Note the tips here of how to setup ssh keys: http://genomewiki.ucsc.edu/index.php/...
user avatar
2 votes
Accepted

replacing periods with hyphen

In A2M format, upper case letters represent matches, lower case letters represent inserts, dashes represent deletions, and dots (or spaces outside the identifier lines) represent gaps aligned to ...
user avatar
1 vote

annotation using ChIPseeker package error

that was solved by changing seq level: ...
user avatar
  • 95
1 vote

ANNOVAR, 1000g database calling

That's a warning. Presumably, a match failed ($& is the default Perl variable which holds the result of a match operation). So something in your input is not ...
user avatar
  • 7,957
1 vote

hgsql not found when running a script despite being accessible on command-line

It is possible that the shell being used in the process is different from your standard command line shell. I am not familiar with the tool, and it's hard to say more without knowing your OSX version, ...
user avatar
1 vote
Accepted

Where can I find the DNA sequence of the C. elegans rRNA cluster?

The info is actually in the gene_biotype column of my wormGenes data frame. I could select the rRNA genes using ...
user avatar
1 vote

Help Adjusting Bedtools Output in R

In case an answer would still be relevant after a year and a half, below is a solution with the Biostrings package. ...
user avatar
  • 3,472
1 vote
Accepted

Why does RATT create a directory with chromosome sequences and how can I stop it?

RATT seems to be a very simple wrapper script that unfortunately does not clean up its temporary files properly. Short of modifying the code yourself, your only option is to perform the cleanup ...
user avatar
1 vote

Software recommendation: find DNA sequence distribution over entire transcript

I assume you have the sequence in seq1: ...
user avatar
  • 4,622

Only top scored, non community-wiki answers of a minimum length are eligible