User: cmdcolin

gravatar for cmdcolin
cmdcolin930
Reputation:
930
Status:
Trusted
Location:
United States
Website:
https://github.com/cmd...
Last seen:
12 hours ago
Joined:
6 years, 1 month ago
Email:
c**********@gmail.com

Computer Science MS student

JBrowse core developer

 

Past:

 

Computer Science BS at University of Colorado
Research assistant at University of Missouri
Research assistant at Michigan State University

Posts by cmdcolin

<prev • 168 results • page 1 of 17 • next >
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Comment: C: 3' UTR FASTA back to genes
... Is there any reason why the 3' UTRs are fully unassociated with any gene? ...
written 13 days ago by cmdcolin930
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Comment: C: Filter VCF by sample?
... Thanks again for this answer. Finding my own questions in a google search now 2 years later. Note that a relatively recent version of bcftools should be used e.g. the one from htslib simple because the options like --min-ac don't exist in the old 0.1.19 from the samtools package. If someone just wan ...
written 22 days ago by cmdcolin930
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Comment: C: So frustrated compiling necessary packages in a linux system
... linuxbrew/homebrew at least need git installed ...
written 4 weeks ago by cmdcolin930
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Answer: A: Extracting Read Pairs From Region So That All Pairs Remain Intact
... A new software called Bazam is built for doing this type of task https://github.com/ssadedin/bazam It is designed to output a FASTQ for realignment and doesn't re-output the original BAM data as currently implemented I think but I made a request to maybe enable BAM/SAM output of the tool. Preprint ...
written 4 weeks ago by cmdcolin930
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Comment: C: Extracting Read Pairs From Region So That All Pairs Remain Intact
... Would love a good script that handles step 2 ...
written 4 weeks ago by cmdcolin930
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Comment: C: 4/6 genotype in VCF
... The alternative alleles can contain multiple letters so this assertion that it is less that the "base space" e.g. ACGT is false. You can see things like alternative_alleles=TC,TCC,TCCC E.g. it can have multiple letters. ...
written 6 weeks ago by cmdcolin930
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Comment: C: Where Can I Download Some Bam Files?
... The links in this interface seem to refer to dead UCSC links now unfortunately (presumably due to referring to hgdownload-test URL). Cool resource though! ...
written 3 months ago by cmdcolin930
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Answer: A: How do I filter my VCF file to only include certain coordinates from a BED file?
... BEDTools has the ability to process VCF (and BED too of course), so you can use "bedtools intersect" with the VCF and BED file as input Hope that helps ...
written 3 months ago by cmdcolin930
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Comment: C: How to customize the looks of dynamically generated tracks in jbrowse?
... I'm using the latest 1.15 version. I tested the 1.12.5 release and can indeed see that this version does not plot subfeatures like your screenshot has. I can't recall exactly what would be the thing that changed that fixed this per se but if you can upgrade you might consider that! ...
written 3 months ago by cmdcolin930
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Comment: C: How to order a gff3 file by coordinates
... The genometools command `gt gff3 -sort yourfile.gff > yourfile.sorted.gff` is also available and uses a slightly different algorithm than sortlines. Could be of interest ...
written 3 months ago by cmdcolin930

Latest awards to cmdcolin

Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Popular Question 21 days ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Filter VCF by sample?
Scholar 3 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 5 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Popular Question 7 months ago, created a question with more than 1,000 views. For Filter VCF by sample?
Appreciated 14 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 18 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 18 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 18 months ago, created 100 posts.
Appreciated 19 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 23 months ago, voted more than 100 times.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 3.9 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 4.0 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Supporter 4.1 years ago, voted at least 25 times.
Autobiographer 4.3 years ago, has more than 80 characters in the information field of the user's profile.

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