User: cmdcolin

gravatar for cmdcolin
cmdcolin330
Reputation:
330
Status:
Trusted
Location:
United States
Website:
https://github.com/cmd...
Last seen:
21 hours ago
Joined:
4 years, 4 months ago
Email:
c**********@gmail.com

Bioinformatics at MSU

Posts by cmdcolin

<prev • 71 results • page 1 of 8 • next >
0
votes
0
answers
68
views
0
answers
Comment: C: Convert bed12 to GFF
... I was checking out this file http://www.igbquickload.org/blueberry/V_corymbosum_Aug_2015/augustus-take6.bed.gz ...
written 8 days ago by cmdcolin330
0
votes
0
answers
68
views
0
answers
Comment: C: Convert bed12 to GFF
... I was able to get the BED_to_GFF app that I assume the raetsch lab created at the galaxy server here to work https://galaxy.inf.ethz.ch/ but it is corrupt (the children have same ID as parents) and outputs gtf/gff2 instead of gff3 ...
written 9 days ago by cmdcolin330
0
votes
0
answers
68
views
0
answers
Comment: C: Convert bed12 to GFF
... Hi there, I tried out genometools "gt bed_to_gff3 file.bed > out.gff" but it is giving a funny error about "gt bed_to_gff3: error: file "file.bed": line 116470: BED feature has length 0" but the file does not have a line 116470, it is only half that many lines. I dunno where to check for debuggin ...
written 9 days ago by cmdcolin330
1
vote
0
answers
68
views
0
answers
Convert bed12 to GFF
... There are several posts online about converting a GFF/GTF to BED12 but is there any way to go the other direction and convert BED12 to GFF? ...
bed gff bed12 written 9 days ago by cmdcolin330
0
votes
1
answer
109
views
1
answers
Comment: C: Split a BAM within a chromosome without losing read pairs
... It would be highly likely that name sorting it first and then splitting will be much much easier as pairs have the same name in a BAM file! ...
written 15 days ago by cmdcolin330
0
votes
2
answers
189
views
2
answers
Answer: A: Extracting entries from GTF file
... You may like to use tabix. Tabix has a setting that works well with GFF, so I would convert the GTF to GFF (probably using gffread from cufflinks package, for example `gffread -E merged.gtf -o- > merged.gff3`) Then you can bgzip and tabix the output bgzip myfile.sorted.gff tabix -p gff ...
written 4 weeks ago by cmdcolin330
0
votes
0
answers
166
views
0
answers
Comment: C: Perl::ForkManager does not speed up ATCG calculation !!
... note: I didn't mean to sound so negative and offtopic in this reply as I know the forkmanager was really the topic in question :) ...
written 4 weeks ago by cmdcolin330
1
vote
0
answers
166
views
0
answers
Comment: C: Perl::ForkManager does not speed up ATCG calculation !!
... The way that you calculate the percentages is not efficient in check ACGT, using repeated regexes over the entire sequence simply to count number of characters, where it could simply loop through the string to count characters or similar. I can't comment on how the ForkManager works but that to me i ...
written 4 weeks ago by cmdcolin330
0
votes
1
answer
169
views
1
answers
Comment: C: install augustus on MAC
... In general with homebrew you don't want to use sudo to install things anymore, so you can use `sudo chown -R username:admin /usr/local/` which will try to reset permissions to you in /usr/local. You can also run `brew doctor` which will probably tell you to run something similar ...
written 4 weeks ago by cmdcolin330
0
votes
1
answer
169
views
1
answers
Answer: A: install augustus on MAC
... It is hard to read these error messages, but in general, I would suggest installing augustus with Homebrew. See http://brew.sh/ brew install homebrew/science/augustus You can also look at the "formula" that Homebrew uses to install augustus and it's dependencies in detail here https://github. ...
written 4 weeks ago by cmdcolin330

Latest awards to cmdcolin

Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 11 weeks ago, voted more than 100 times.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 2.2 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 2.3 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Supporter 2.4 years ago, voted at least 25 times.
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 475 users visited in the last hour