User: cmdcolin

gravatar for cmdcolin
cmdcolin1.3k
Reputation:
1,300
Status:
Trusted
Location:
United States
Website:
https://github.com/cmd...
Last seen:
3 hours ago
Joined:
7 years, 5 months ago
Email:
c**********@gmail.com

JBrowse developer

 

Posts by cmdcolin

<prev • 229 results • page 1 of 23 • next >
0
votes
1
answer
74
views
1
answers
Comment: C: warning when creating salmon index from GENCODE transcriptome
... It is generally just a weird thing where the "format of FASTA headers" is always just some gobbledegook freeform text basically, so it is not generally a weird thing to "suggest special handling" like this, it is actually nice. If you want to see about the effect of reference genome on your analysis ...
written 5 weeks ago by cmdcolin1.3k
0
votes
0
answers
426
views
0
answers
Comment: C: Twist Bioscience BAM example
... Can search at SRA for twist biosciences https://www.ncbi.nlm.nih.gov/sra/?term=twist I wish there was a nice BAM available for quick checking but can see if SRA will help ...
written 5 weeks ago by cmdcolin1.3k
0
votes
4
answers
33k
views
4
answers
Comment: C: What are chimeric reads?
... possibly here now https://drive5.com/usearch/manual/chimeras.html ...
written 6 weeks ago by cmdcolin1.3k
0
votes
5
answers
1.8k
views
5
answers
Comment: C: Interesting/useful/beautiful bio sequence viz tools
... Sure, PRs are welcome. I added a little contributing.md file, basically anything is welcome though ...
written 7 weeks ago by cmdcolin1.3k
0
votes
5
answers
1.8k
views
5
answers
Comment: C: Interesting/useful/beautiful bio sequence viz tools
... I started a large list here of lots of different types of viewers https://github.com/cmdcolin/awesome-genome-visualization/blob/master/README.md ...
written 7 weeks ago by cmdcolin1.3k
0
votes
2
answers
819
views
2
answers
Answer: A: How To Fetch Exon Sequence From Genomic Coordinates
... The gffread which has special tools for extracting the sequence given a gff and a reference seq http://ccb.jhu.edu/software/stringtie/gff.shtml ...
written 9 weeks ago by cmdcolin1.3k
0
votes
3
answers
35k
views
3
answers
Comment: C: Adding Read Groups To Bam Files
... Thanks for the note on escaping the @ character...was really confused ...
written 10 weeks ago by cmdcolin1.3k
1
vote
7
answers
13k
views
7
answers
Answer: A: Other Genomic Viewer Like Igv
... I started a large list of genome browsers and general genome data viz software here https://github.com/cmdcolin/awesome-genome-visualization/ Includes mostly genome browser type things but some others (dotplots, msa, etc) ...
written 11 weeks ago by cmdcolin1.3k
0
votes
0
answers
138
views
0
answers
Comment: C: How to use mummer's output for visualization ?
... I do recognize that mummer can output SNP, but probably other tools are easier to use ...
written 11 weeks ago by cmdcolin1.3k
0
votes
0
answers
138
views
0
answers
Comment: C: How to use mummer's output for visualization ?
... Are you aligning reads? Why not use a tool more built for aligning reads and then outputs SAM/BAM so that you can just view coverage in genome browser? ...
written 11 weeks ago by cmdcolin1.3k

Latest awards to cmdcolin

Appreciated 6 weeks ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Student 9 weeks ago, asked a question with at least 3 up-votes. For Filter VCF by sample?
Popular Question 3 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Popular Question 3 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Popular Question 4 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Scholar 4 months ago, created an answer that has been accepted. For A: Reshape tabular data frame to wide format
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 12 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 13 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 14 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Guru 14 months ago, received more than 100 upvotes.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Popular Question 17 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Popular Question 19 months ago, created a question with more than 1,000 views. For Filter VCF by sample?
Scholar 20 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 22 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Filter VCF by sample?
Appreciated 2.5 years ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 2.9 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 2.9 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1156 users visited in the last hour