User: genecats.ucsc

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genecats.ucsc500
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Posts by genecats.ucsc

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Repeat names with "dup" at the end in repeatMasker GTF (UCSC) file?
... Sorry for the late reply but yes that is correct. The problem here is the GTF output function from the Table Browser, there have been issues with that specific function for a long time. If you want you can just download the rmsk table and work on it directly: http://hgdownload.cse.ucsc.edu/goldenPa ...
written 3 months ago by genecats.ucsc500
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Answer: A: Repeat names with "dup" at the end in repeatMasker GTF (UCSC) file?
... Here are the first few lines from the rmsk table for hg38, where I have filtered for items like "ERV24B": #filter: (repName like 'ERV24B%') #bin swScore milliDiv milliDel milliIns genoName genoStart genoEnd genoLeft strand repName repClass repFamily repStart repEnd repLeft id 675 1260 2 ...
written 3 months ago by genecats.ucsc500
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Answer: A: Download EST spliced alignments UCSC
... It is possible to generate those alignments with the pslPretty utility, available from our list of utilities: http://hgdownload.soe.ucsc.edu/admin/exe Here is an example where I also illustrate some other useful commands, faSomeRecords and pslSomeRecords, which are also available from the same dire ...
written 3 months ago by genecats.ucsc500
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Answer: A: Get UCSC Genome Browser assembly ID
... Genomax already answered, but here is also a mysql command you can use if you don't want to download the entire hgcentral database dump: $ mysql -h genome-mysql.soe.ucsc.edu -u genome -e "select name, scientificName from dbDb limit 5" hgcentral +---------+----------------------------------- ...
written 4 months ago by genecats.ucsc500
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Answer: A: Question on UCSC genome browser display
... If you reset your cart (Genome Browser->Reset all user settings in the top blue menu bar) and then go back to the Genome Browser, when you shift+click, a dialog box should come up explaining different zooming and highlighting keyboard shortcuts as well as some highlighting options. There is also ...
written 4 months ago by genecats.ucsc500
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Answer: A: Wig file interpreted as bed file in genome browser
... As genomax said, you need to add a track definition line when you load your custom track, something like: track type=bigWig name="Example Name" description="Example Description" http://url.to.your/file Here's a list of the different track types supported: http://genome.ucsc.edu/goldenPath/ ...
written 4 months ago by genecats.ucsc500
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Comment: C: wig files to bigwig using UCSC kent
... This error happens when you have wiggle lines like the following: variableStep chrom=chromName span=5 1000 0.56 1001 0.55 In this case the positions 1000-1004 are supposed to have the value 0.56 but then on the next line positions 1001-1005 are supposed to have value 0.55, and since a ...
written 5 months ago by genecats.ucsc500
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Comment: C: wig files to bigwig using UCSC kent
... Yes what are the other chrom lines like in the wiggle file though? Do all the chromosome names correspond to what is the chrom.sizes file? Try grepping for 'chr2' from your wiggle file and see what shows up. Or something like this to get only the chromosome names: $ grep chrom userWig2.wig | c ...
written 5 months ago by genecats.ucsc500
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Answer: A: wig files to bigwig using UCSC kent
... You need to make sure that all of the chromosome names in your wiggle file are accounted for in the chrom.sizes file. For instance, if my wiggle file looks like this: variableStep chrom=chr2CEN 3003560 0 And my chrom.sizes file looks like this: chr2CEN 242193529 Then I can still run ...
written 5 months ago by genecats.ucsc500
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Comment: C: wigCorrelate Error "Please remove overlaps and try again"
... Hi Samad, wigToBigWig works fine for me with the following test wiggle file: $ cat test.wig variableStep chrom=chr1 3003560 0 3003561 0 3003562 0 3003563 0 $ wigToBigWig test.wig hg38.chrom.sizes out.bw What commands are you running to generate a bigWig? Additionall ...
written 5 months ago by genecats.ucsc500

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