User: max

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max40
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Posts by max

<prev • 13 results • page 1 of 2 • next >
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Comment: A: ucsc ids conversion
... Can you explain a little why you want UCSC IDs? Note that UCSC Ids are not created anymore, UCSC defaults to Gencode IDs now. See the UCSC Genes FAQ: https://genome.ucsc.edu/FAQ/FAQgenes.html#hg19 ...
written 4 weeks ago by max40
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Answer: A: Naming Chromosomes: From Ncbi Nc_0000Abc To Ucsc Chrabc
... Historically there are small differences in the way that NCBI, EBI and UCSC name the chromosomes. What is "MT" for EBI, is called "chrMT" for NCBI and "chrM" for UCSC. If you used a genome not from UCSC for your analysis, you may have to fix up these small differences. To do this converation on a te ...
written 4 weeks ago by max40
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Answer: A: How To Convert Chromosome Names Of Ensembl Annotation To The Ones Of Ucsc Refseq
... Note that historically there are small differences in the way that NCBI, EBI and UCSC name the chromosomes. What is "MT" for EBI, is called "chrMT" for NCBI and "chrM" for UCSC. If you used a genome not from UCSC for your analysis, you may have to fix up these small differences. To convert EBI or NC ...
written 4 weeks ago by max40
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Comment: C: bedGraphToBigWig Tutorial and Report
... Note that historically there are small differences in the way that NCBI, EBI and UCSC name the chromosomes. What is "MT" for EBI, is called "chrMT" for NCBI and "chrM" for UCSC. If you used a genome not from UCSC for your analysis, you may have to fix up these small differences. To convert EBI or NC ...
written 4 weeks ago by max40
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Answer: A: bedGrapthToBigWig conversion, xxx is not found in chromosome files
... Due to history, there are small differences in the way that NCBI, EBI and UCSC name the chromosomes. What is "MT" for EBI, can be "chrMT" for NCBI and "chrM" for UCSC. To convert your NCBI to UCSC chrom names, use UCSC's little utility chromToUcsc. Download it with "wget https://hgdownload.soe.ucsc. ...
written 4 weeks ago by max40
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Comment: A: how to merge overlapping intervals in a bedgraph file
... the UCSC kent tools include a tool bedRemoveOverlap. It doesn't summarize, it just cleans up, which in most cases what I need, as the overlaps will be <0.01% of all features. ...
written 3 months ago by max40
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Answer: A: a webserver for the bigwig files
... See the UCSC docs https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting One free option, at reduced speed, is Cyverse. Two other free options, with higher speed but limited file sizes, are Figshare and Github. As for the paid options, the UCSC page says this: --- In general, commer ...
written 13 months ago by max40
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Answer: A: BWA ALN cannot not find a very obvious match
... Sorry, this was stupid. I have to run bwa samse like this to get all matches: "bwa samse -n 100000000". Never mind. ...
written 19 months ago by max40
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Solved: BWA ALN cannot not find a very obvious match
... (Originally from Milan Simonovic posted on sourceforge but I could reproduce it and have the same problem, https://sourceforge.net/p/bio-bwa/mailman/message/36190558/) We have BWA at full sensitivity here and it still cannot find a very obvious sequence in zebrafish chr10. Any ideas what we're miss ...
alignment sam bwa written 19 months ago by max40 • updated 19 months ago by genomax80k
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Answer: A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
... Use the UCSC Data Integrator to intersect two tables and keep both fields: https://genome.ucsc.edu/cgi-bin/hgIntegrator ...
written 2.2 years ago by max40

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