User: genecats.ucsc

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genecats.ucsc420
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Please know UCSC supports several lists where users can email questions and search archived answers:

-For posting general non-mirror and non-confidential questions: * Post to the Public Help Forum: Email genome@soe.ucsc.edu or Search the Public Archives: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome

-For posting mirror-specific questions: * Post to the Mirror Help Forum: Email genome-mirror@soe.ucsc.edu or Search the Mirror Archives : https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror

-For posting questions with information that is private/confidential: * Email genome-www@soe.ucsc.edu

Posts by genecats.ucsc

<prev • 32 results • page 1 of 4 • next >
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Answer: A: How to find the chromosomal coordinate of a mutation in a gene?
... If this is for some Human assembly you can make an HGVS term out of your information and paste into the search box on the UCSC Genome Browser. The highlighted base(s) will be your mutation coordinate(s). If you have further questions about UCSC data or tools feel free to send your question to one o ...
written 21 days ago by genecats.ucsc420
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Comment: C: genepredtogtf command fails
... What are the first few lines of XGenome.txt? ...
written 22 days ago by genecats.ucsc420
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Comment: C: UCSC Fasta files by chromosome for rn6
... We make these individual chromosome files when the chromosome count is under 100. Most assemblies these days have over 100 chromosomes and so we don't run them up anymore. ...
written 5 weeks ago by genecats.ucsc420
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Answer: A: UCSC Fasta files by chromosome for rn6
... The UCSC utility twoBitToFa can get the sequence for an individual chromosome at a time via the -seq option, which you can run in a loop for each chromosome: $ wget http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/rn6.chrom.sizes $ for chr in $(cut -f1 rn6.chrom.sizes); do twoBitT ...
written 5 weeks ago by genecats.ucsc420
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Answer: A: GTF file for reference
... If you would like to "edit" your UCSC Table Browser obtained GTF file, we have provided some utilities to do so: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format The basic gist is to download your table of interest, chop off some columns (may or may not be necessary depending on the ...
written 6 weeks ago by genecats.ucsc420
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Answer: A: Converting GTF file to UCSC-styled bed file
... There is a UCSC utility for this purpose, gtfToGenePred, which can be downloaded from the directory appropriate to your operating system here: http://hgdownload.soe.ucsc.edu/admin/exe/ Here is a page (which mostly describes converting in the opposite direction, genePred to gtf), that describes some ...
written 6 weeks ago by genecats.ucsc420
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Answer: A: Why genomic information shown in UCSC/Ensembl browser for a specific gene is dif
... 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 8 weeks ago by genecats.ucsc420
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Answer: A: HG19 Annotation download with Gene Names.
... 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 9 weeks ago by genecats.ucsc420
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Answer: A: fixedStep or variableStep Smoothening wig file
... 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 9 weeks ago by genecats.ucsc420
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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 9 weeks ago by genecats.ucsc420

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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Batch download of hg19 sequences in bed file
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