SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 10 of 10
Search took 0.00 seconds.
Search: Posts Made By: rhubley
Forum: Bioinformatics 06-28-2013, 08:04 AM
Replies: 11
Views: 9,433
Posted By rhubley
Yes. You can use the...

Yes. You can use the RepeatMasker/util/buildSummary.pl script to reprocess the *.out file and summarize the results. The buildSummary.pl creates a similar table to the *.tbl file but also includes...
Forum: Bioinformatics 06-19-2013, 11:11 AM
Replies: 15
Views: 7,822
Posted By rhubley
Hi Ben, That's an interesting find. ...

Hi Ben,

That's an interesting find. Alke's filter-stage-1.prl script should be better at reporting when it cannot find a dependent program. I added the following code to the script:

use...
Forum: Bioinformatics 06-12-2013, 08:40 PM
Replies: 1
Views: 1,763
Posted By rhubley
It looks like you have some strange characters at...

It looks like you have some strange characters at the end of these lines in your FASTA file. Open the file in a editor and double check the format of these sequences.
Forum: Bioinformatics 06-12-2013, 10:03 AM
Replies: 15
Views: 7,822
Posted By rhubley
Hi Ben, RepeatScout is a great program for...

Hi Ben,

RepeatScout is a great program for finding highly conserved repetitive elements. As a consequence we run RepeatScout first ( and only one round ) in order to find and remove the young...
Forum: Bioinformatics 06-12-2013, 09:39 AM
Replies: 3
Views: 2,044
Posted By rhubley
Sorry, I didn't see the "?" in your original...

Sorry, I didn't see the "?" in your original question. The "?" following either a class for subclass is an indication that the curator is not confident in the call of the class or subclass. As we...
Forum: Bioinformatics 06-11-2013, 01:08 PM
Replies: 11
Views: 9,433
Posted By rhubley
Check out the util/buildRMLibFromEMBL.pl script...

Check out the util/buildRMLibFromEMBL.pl script included in the RepeatMasker distribution. This will convert the RepeatMaskerLib.embl file into a fasta file with the "#class/subclass" nomenclature.
Forum: Bioinformatics 06-11-2013, 11:41 AM
Replies: 11
Views: 9,433
Posted By rhubley
RepeatClassifier can be run independently. If...

RepeatClassifier can be run independently. If you hand it a fasta file it will generate a new file with a *.classified suffix. The output file will be a fasta file with all the id#class/subclass...
Forum: Bioinformatics 06-11-2013, 11:06 AM
Replies: 3
Views: 2,044
Posted By rhubley
The "DNA" class stands for DNA Tranposon -- a cut...

The "DNA" class stands for DNA Tranposon -- a cut and paste type of interspersed repeats.
Forum: Bioinformatics 09-11-2012, 04:26 PM
Replies: 3
Views: 2,389
Posted By rhubley
Family/Subfamily Designations

The "?" Following either a the family or the subfamily designations is an indication by the sequence curator that the assignment may be questionable. Over time as the repeat library improves these...
Forum: Bioinformatics 09-11-2012, 11:40 AM
Replies: 14
Views: 4,961
Posted By rhubley
A user just pointed out this forum to us. We are...

A user just pointed out this forum to us. We are sorry to hear that people have been having problems running RepeatMasker. Luckily with this user's help we tracked down the problem and have a fix...
Showing results 1 to 10 of 10

 


All times are GMT -8. The time now is 08:33 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO