User: cmdcolin

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cmdcolin1.2k
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JBrowse developer

 

Posts by cmdcolin

<prev • 208 results • page 1 of 21 • next >
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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 10 days ago by cmdcolin1.2k
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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 21 days ago by cmdcolin1.2k
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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 21 days ago by cmdcolin1.2k
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Comment: C: Distinguishing between different formats for VCF file indexes
... Probably you can tell by the file extension. IDX is a "tribble index" and TBI is a tabix index ...
written 26 days ago by cmdcolin1.2k
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Comment: C: How to clean this strange VCF file?
... 0/0 and ./. actually mean different things (this was a surprise to me at one point also). The ./. indicates no-call/no-call e.g. the variant caller made no determination, and 0/0 is homozygous ref. I don't know why you would have haploid things with just "0" in the first column ...
written 28 days ago by cmdcolin1.2k
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Comment: C: JBrowse help with opening a Gff gene model file
... What browser are you using? I do not get any error doing this in a local instance ...
written 5 weeks ago by cmdcolin1.2k
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Comment: C: JBrowse help with opening a Gff gene model file
... I am presuming you mean convert to json using bin/flatfile-to-json.pl --gff yourfile.gff --trackLabel. Just wanted to clarify that in case it was unclear for Hwaterma ...
written 5 weeks ago by cmdcolin1.2k
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Comment: C: How To Merge Gff Files
... Programs such as MAKER combine evidence for gene models ...
written 5 weeks ago by cmdcolin1.2k
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Comment: C: JBrowse help with opening a Gff gene model file
... How is this track opened? Did you use the Track->Open track inside JBrowse or loaded via command line? Also the formatting on this gff is messed up by posting so it's hard to tell if it's formatted right, but a cursory look appears to not have anything wrong ...
written 6 weeks ago by cmdcolin1.2k
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Comment: C: JBrowse help with opening a Gff gene model file
... Hi Hwaterma, I'm a JBrowse dev. It is hard to debug this without more info. If you can share any more data or info about your setup let me know ...
written 6 weeks ago by cmdcolin1.2k

Latest awards to cmdcolin

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 3 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 5 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 5 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
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Popular Question 8 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Popular Question 10 months ago, created a question with more than 1,000 views. For Filter VCF by sample?
Scholar 12 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 13 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Popular Question 16 months ago, created a question with more than 1,000 views. For Filter VCF by sample?
Appreciated 22 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
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
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Appreciated 2.3 years ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
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Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
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