User: cmdcolin

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cmdcolin1.4k
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JBrowse developer

 

Posts by cmdcolin

<prev • 235 results • page 1 of 24 • next >
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Answer: A: Does 1000 genomes have a flat file with allele frequencies for each site anywher
... Might look at ALFA Ref https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/ Some flatfiles, run bigBedToBed to convert to bed https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/ Read https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/ALFA.html ...
written 6 weeks ago by cmdcolin1.4k
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Answer: A: Why does bioinformatics use a special format like a BAM file instead of a databa
... If none of the arguments are convincing, BAM (and CRAM) files also have a nice quality of being remotely accessible in slices (query genomic ranges) via HTTP with zero SQL server setup or REST API. This makes it much easier for users to access their alignment data remotely over ftp and http, users c ...
written 9 weeks ago by cmdcolin1.4k
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Comment: C: Jbrowse: importance of draw-basepair-track.pl
... note for future generations you might consider the sashimiplot plugin https://github.com/elsiklab/sashimiplot/ it renders arcs in JS instead of pre-rendering to disk with libgd ...
written 3 months ago by cmdcolin1.4k
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Comment: C: Nanopore structural variant calling - more than 2 alleles on IGV track?
... do you have a sample of the VCF being displayed? ...
written 5 months ago by cmdcolin1.4k
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Answer: A: Merge two bigwig(+/- strand) files from RNA-seq
... I think the question is not really about merging the files, which is not really possible since bigwig only allows one signal per file Therefore we really want to display multiple bigwigs on a single track. This can be done via jbrowse with the multibigwig plugin (https://github.com/elsiklab/multibi ...
written 5 months ago by cmdcolin1.4k
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Strategy for 2D interval query?
... Hi there This is a bit conceptual but say I wanted to compare human and mouse, looking at human chr1 and chr2 and mouse chr1 and chr2. This would look like so human chr1 chr2 +-----------+ --------+ | ...
bedpe comparative-genomics conceptual written 5 months ago by cmdcolin1.4k
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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 8 months ago by cmdcolin1.4k
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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 8 months ago by cmdcolin1.4k
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Comment: C: What are chimeric reads?
... possibly here now https://drive5.com/usearch/manual/chimeras.html ...
written 8 months ago by cmdcolin1.4k
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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 8 months ago by cmdcolin1.4k

Latest awards to cmdcolin

Appreciated 9 weeks ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Ideal settings for blasting a protein/cdna against a genome?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Piping bowtie2 output directly into BAM
Appreciated 8 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Student 9 months ago, asked a question with at least 3 up-votes. For Filter VCF by sample?
Popular Question 10 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 Convert bed12 to GFF
Popular Question 10 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Scholar 11 months ago, created an answer that has been accepted. For A: Reshape tabular data frame to wide format
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 19 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
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 20 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Guru 21 months ago, received more than 100 upvotes.
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Popular Question 24 months ago, created a question with more than 1,000 views. For Convert bed12 to GFF
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Filter VCF by sample?
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 2.4 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Filter VCF by sample?
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back

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