User: genecats.ucsc
genecats.ucsc • 340
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Posts by genecats.ucsc
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... Our data tables store data for each transcript (one row per transcript generally), and since multiple transcripts can be associated with the same gene symbol, when you download data for a particular gene symbol, you will get all of the transcripts associated with that gene symbol, and not just one. ...
written 6 days ago by
genecats.ucsc • 340
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... This information is in the name2 field of the refGene table for hg19. Here is a command to swap the name column with the name2 column and get a bed file with the "right" name for IGV:
$ mysql -h genome-mysql.soe.ucsc.edu -ugenomep -ppassword -Ne "select * from refGene where name2='HLA-A'" hg19 | cu ...
written 11 days ago by
genecats.ucsc • 340
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... You can smooth the display of your wiggle files via the wiggle track user interface on the UCSC Genome Browser:
1. Upload your wiggle
2. Once the track is displayed, right click on the track
3. Find the text "Smoothing window" and in the dropdown list next to it, select the number of pixels to ...
written 12 days ago by
genecats.ucsc • 340
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Answer:
A: chrom.sizes computed locally
... The chrom.sizes file is computed in the following way for all assemblies at UCSC:
faToTwoBit organism.fa organism.2bit
twoBitInfo out.2bit stdout | sort -k2rn > organism.chrom.sizes
If you know the URL to a 2bit file we've already made, twoBitInfo accepts a URL like so:
twoBitInfo -udcDir=. htt ...
written 12 days ago by
genecats.ucsc • 340
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... Liftover will work just fine for bacterial sequences as long as you have created the liftover chain files for the alignment between the two genomes. Making these liftover chains is not trivial, but here is some information on the process:
http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_h ...
written 20 days ago by
genecats.ucsc • 340
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Comment:
C: Genome Browser suggestions
... Was there anything in particular that was too slow? I can create a bug report for it if there was something specific.
Thanks,
ChrisL from the UCSC Genome Browser ...
written 24 days ago by
genecats.ucsc • 340
1
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... The issue here is that the transcript you are interested in lies on the negative strand, and so the Table Browser returns a reverse complemented sequence compared to what you are seeing from DAS, which is a simple genomic query. If you reverse complement one of the sequences you will find that they ...
written 4 weeks ago by
genecats.ucsc • 340
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... bedClip is a command line program to do this:
bedClip input.bed http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes output.bed
You can download bedClip from the directory appropriate to your operating system within our [directory of utilities][1].
If you have questions about ...
written 12 weeks ago by
genecats.ucsc • 340
1
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... This sounds like the perfect use case for our GBiB product, it is a fully self-contained UCSC Genome Browser that runs on your own personal machine.
After downloading the machine, you can [share a folder][1] with your BAM file in it, and then view your BAM file just fine! It sounds like you already ...
written 12 weeks ago by
genecats.ucsc • 340
3
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1
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249
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... If your organism of interest is Human, then the [Variant Annotation Integrator][1] (VAI) at the UCSC Genome Browser can get these rsID's for you. Load your VCF file as a custom track, head to the VAI, make whatever selections you want, then make sure the "Include dbSNP rs# ID if one exists" box is c ...
written 3 months ago by
genecats.ucsc • 340
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For A: Batch download of hg19 sequences in bed file
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For A: Batch download of hg19 sequences in bed file
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