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 ...
- 4,898
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....
- 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 ...
- 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 ...
- 4,745
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 ...
- 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 <...
- 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 ...
- 4,898
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 ...
- 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 ...
- 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:
...
- 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 ...
- 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 ...
- 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 ...
- 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 ...
- 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/...
- 81
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 ...
- 56
1
vote
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 ...
- 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, ...
- 2,547
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 ...
- 2,319
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.
...
- 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 ...
- 4,745
1
vote
Software recommendation: find DNA sequence distribution over entire transcript
I assume you have the sequence in seq1:
...
- 4,622
Only top scored, non community-wiki answers of a minimum length are eligible