User: Felix

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Felix50
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6 years, 2 months ago
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6 years, 6 months ago
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Posts by Felix

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Human Genome 18 Converter
... Just to make the list complete: There is also the NCBI remapper: http://www.ncbi.nlm.nih.gov/genome/tools/remap ...
written 6.2 years ago by Felix50
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Comment: C: Gencode Annotations For 44 Regions Of The Human Genome
... Please note these version 3,4,7 are NOT the pilot phase data sets. The pilot phase website is here: http://www.sanger.ac.uk/resources/databases/encode/pilot.html and the data can be visualized when you do a track search for GENCODE or EGASP on the UCSC hg18 assembly. The website for the main phase o ...
written 6.3 years ago by Felix50
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Answer: A: De-Novo Genome Assembly Vs Comparative Genome Assembly
... It also depends on the sequencing depth of the newly sequenced genome. If you only have a low coverage (maybe <6x) the de-novo assembly quality will be dubious. I believe combining the two approaches would be the better strategy in this case. ...
written 6.4 years ago by Felix50
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Answer: A: Gff3 Format - Human Genome
... You can also get all Ensembl data including gene annotation GTFs (which you can convert to GFF3) from here: http://www.ensembl.org/info/data/ftp/index.html. Through their BioMart you can customize your search and download e.g. a CVS file. ...
written 6.4 years ago by Felix50
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Answer: A: Comprehensive Gene Sets
... One thing that many people might not realize is the relation between Ensembl, Vega/Havana and Gencode. Through the Gencode project, Ensembl now incorporates the manual gene annotation provided by Vega/Havana into the automatic annotation. For most cases the data is the same between Ensembl (fetched ...
written 6.5 years ago by Felix50
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Answer: A: Human Exome Capture Library Coordinates Download
... Before you try re-creating the entire region list, please use the files at ftp://ftp.sanger.ac.uk/pub/fsk/exome/ e.g. exome_B_NCBI36.bed. These are the regions the Agilent design was targetted at, created by merging coding regions of Havana and Ensembl genes (not just CCDS genes), adding miRNAs and ...
written 6.5 years ago by Felix50

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