User: genecats.ucsc

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genecats.ucsc460
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Posts by genecats.ucsc

<prev • 41 results • page 1 of 5 • next >
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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 4 days ago by genecats.ucsc460
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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 days ago by genecats.ucsc460
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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 days ago by genecats.ucsc460
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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 days ago by genecats.ucsc460
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Comment: C: how to get cruzbd (cds_sequence) dna translation
... For that particular transcript, you are in the UTR: https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg38_utrGp6 The position you are interested in is the blue highlight. The reason you see translation in the Multiz 100 way t ...
written 4 weeks ago by genecats.ucsc460
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Answer: A: how to get cruzbd (cds_sequence) dna translation
... Woops sorry, see my reply. ...
written 4 weeks ago by genecats.ucsc460
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Answer: A: how to get cruzbd (cds_sequence) dna translation
... The first issue here is the coordinates you are interested in are on the negative strand, so you'll want to reverse complement the dna you obtain before trying to translate it. Secondly, you can do all of this via UCSC tools like so: $ twoBitToFa -seq=chr19 -start=55014735 -end=55014753 http:/ ...
written 4 weeks ago by genecats.ucsc460
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Answer: A: Distinguishing coding DNA using NCBI and UCSC databases
... We always store our coordinates in relation to the positive strand, because it makes coordinate math easier to deal with. When you click on the transcript in question, you can see the following information: Position: hg38 chr2:178,525,989-178,807,423 Size: 281,435 Total Exon Count: 191 Strand: - Th ...
written 5 weeks ago by genecats.ucsc460
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Answer: A: Create Chromosome Ideogram w/ out reference genome
... Usually the chromosome ideograms at UCSC indicate results of Giemsa staining experiments, not gene locations. If you want to get a whole chromosome view of your data you could create an assembly hub, and create a simple 3 column bigBed file out of your data file, and the just look at the whole chro ...
written 7 weeks ago by genecats.ucsc460
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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 12 weeks ago by genecats.ucsc460

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