User: cmdcolin

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cmdcolin1.0k
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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 • 182 results • page 1 of 19 • next >
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Answer: A: Finding Gene Name Synonyms
... You might also consider mygene.info curl "http://mygene.info/v3/query?q=CXCL8&species=human&fields=all" If you have jq, you can sort of slice and dice the results. This chooses the top hit (make sure to validate this in whatever case you are in) and picks fields from it Pick some alia ...
written 4 days ago by cmdcolin1.0k
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Answer: A: how to extract per base information (in coverage track of IGV) from .bam file
... You could maybe do this with samtools mpileup The mpileup command gets you most of the way there and then a small script can count number of "A","G","T","C" at each position https://www.biostars.org/p/54278/ ...
written 6 days ago by cmdcolin1.0k
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Answer: A: samtools covert to bam, sort and index all gz.sam
... The question "not sure if it is indexed" is probably not relevant to sorting (indexing only happens after you have sorted bam files) Other options for speedup http://devblog.dnanexus.com/faster-bam-sorting-with-samtools-and-rocksdb/ https://www.basepairtech.com/blog/sorting-bam-files-samtools-vs- ...
written 8 days ago by cmdcolin1.0k
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Answer: A: strand identification from sam file
... To be clear, you should perform a bitwise AND operation on any given number from the flag field so if your flag field is 272, then you say 272 AND 16 which is in binary 0100010000 & 0000010000 = 0000010000 which is "true", and in this case, means the read is reverse strand. if ...
written 10 days ago by cmdcolin1.0k
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Comment: C: Top GitHub repos for biomedicine
... Would be pretty interesting if somehow this addressed the software-by-name or software-by-publication too, as github URL is not necessarily as common if you are citing a tool (if you are presenting a new software it is quite common) ...
written 11 days ago by cmdcolin1.0k
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Comment: C: How To Convert Wgsim Output Into A Vcf File?
... Would also be interested in this... ...
written 11 days ago by cmdcolin1.0k
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Comment: C: JBrowse Error : HTTP 200 when fetching file
... +1 for this. You need to setup a web server, you cannot just double click index.html in your file explorer and have it work even if it appears to work for some very limited cases http://jbrowse.org/docs/faq.html#what-webserver-is-needed-for-jbrowse And indeed, the desktop version is a good option a ...
written 11 days ago by cmdcolin1.0k
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Answer: A: Is there a standard file format for anchored contigs?
... Possibly AGP https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ Also see things like agp2fasta https://www.biostars.org/p/69964/ ...
written 19 days ago by cmdcolin1.0k
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Answer: A: Full genome phyloP scores from UCSC Browser
... A bigwig file for phyloP on hg19 whole genome is here http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP100way/ It's a large 8.9Gb bigwig so I do not necessarily suggest converting this into text format all at once, but you could convert to text using bigWigToBedGraph (or convert small chunks at ...
written 28 days ago by cmdcolin1.0k
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Comment: C: IGV ignoring indexed and sorted .bai file and trying to create a .fai file to vi
... TIL....I always thought you needed the sam-to-bam conversion samtools view -Sb, but this looks like it works ...
written 28 days ago by cmdcolin1.0k

Latest awards to cmdcolin

Guru 4 days ago, received more than 100 upvotes.
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Popular Question 11 weeks 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 Filter VCF by sample?
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 7 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Popular Question 9 months ago, created a question with more than 1,000 views. For Filter VCF by sample?
Appreciated 16 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?
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
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Appreciated 21 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 21 months 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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