User: cmdcolin

gravatar for cmdcolin
cmdcolin1.3k
Reputation:
1,260
Status:
Trusted
Location:
United States
Website:
https://github.com/cmd...
Last seen:
12 hours ago
Joined:
7 years, 1 month ago
Email:
c**********@gmail.com

JBrowse developer

 

Posts by cmdcolin

<prev • 215 results • page 1 of 22 • next >
0
votes
1
answer
81
views
1
answers
Comment: C: Displaying structural variants with JBrowse
... I will send you a link to a signup form soon regarding this ...
written 1 day ago by cmdcolin1.3k
1
vote
1
answer
81
views
1
answers
Answer: A: Displaying structural variants with JBrowse
... JBrowse should be ok with displaying structural variants encoded in VCFTabix. Structural variants in VCF are generally written by having something like in the ALT field, the start column is just the start of the feature and the END=123456 in the INFO field indicates the end of the feature. The int ...
written 7 days ago by cmdcolin1.3k
0
votes
3
answers
1.2k
views
3
answers
Answer: A: Does anybody know how to do a local install of samtools on centos without using
... Download linuxbrew https://docs.brew.sh/Homebrew-on-Linux `brew install samtools` ...
written 10 days ago by cmdcolin1.3k
0
votes
3
answers
1.2k
views
3
answers
Comment: C: Does anybody know how to do a local install of samtools on centos without using
... I'll remove my answer only because it is true that the title contained information about not wanting to use sudo. That said, I find your tone rude, I am just trying to contribute to the community ...
written 10 days ago by cmdcolin1.3k
0
votes
3
answers
1.2k
views
3
answers
Comment: C: Does anybody know how to do a local install of samtools on centos without using
... Note that in 2019, the centos version is samtools 0.1.19, so no CRAM support etc. Recommend linuxbrew for package manager solution on CentOS if new version is needed ...
written 14 days ago by cmdcolin1.3k
1
vote
0
answers
116
views
0
answers
Comment: C: Find structural variants comparing two assemblies
... You could combine something like aligning the de-novo contigs to your reference with minimap2 and then using https://github.com/eldariont/svim ...
written 10 weeks ago by cmdcolin1.3k
0
votes
2
answers
315
views
2
answers
Comment: C: Annotation lifting to a different organism
... The TAIR annotation has the unusual feature that it has "gene" lines with a "Parent" being a protein which is not defined in the file. I recommend filtering Parent= attributes from column 9 for the "gene" lines ...
written 10 weeks ago by cmdcolin1.3k
0
votes
0
answers
136
views
0
answers
Comment: C: How can I find out all the conserved sequence between three genomes
... You can choose to look at it from an angle such as orthogroup finding or multiple whole genome alignment. Multiple whole genome alignment involves something like mauve or multiz UCSC pipeline. Orthologs might involve something like https://github.com/davidemms/OrthoFinder (which itself would involve ...
written 4 months ago by cmdcolin1.3k
0
votes
0
answers
134
views
0
answers
Comment: C: How to calculate z-Score over bins in bam file
... Also I am assuming when you say "tags that map to a bin" you mean "reads that map to a bin" ...
written 4 months ago by cmdcolin1.3k
1
vote
0
answers
134
views
0
answers
Comment: C: How to calculate z-Score over bins in bam file
... This isn't a ready made solution but probably something like bedtools makewindows over whole genome, then bedtools coverage for convert to bedgraph, then compute statistics over the counts in the bedgraph ...
written 4 months ago by cmdcolin1.3k

Latest awards to cmdcolin

Scholar 2 days ago, created an answer that has been accepted. For A: Reshape tabular data frame to wide format
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 7 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 9 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 9 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Guru 10 months ago, received more than 100 upvotes.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Popular Question 12 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Popular Question 14 months ago, created a question with more than 1,000 views. For Filter VCF by sample?
Scholar 15 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 17 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Popular Question 19 months ago, created a question with more than 1,000 views. For Filter VCF by sample?
Appreciated 2.2 years ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 2.5 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 2.5 years ago, created 100 posts.
Appreciated 2.6 years ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 2.9 years ago, voted more than 100 times.
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1496 users visited in the last hour