User: Dan

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Dan500
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Cambridge
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http://metaDatabase.com
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1 year, 4 months ago
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9 years, 6 months ago
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Posts by Dan

<prev • 75 results • page 1 of 8 • next >
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Comment: C: How to represent trans-spliced genes in GTF?
... The issue is with tools that require GTF but not GFF3. ...
written 2.2 years ago by Dan500
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Answer: A: How to dump genes from GenBank in GFF3 format?
... Ha, turns out you can just grab the GFF3 from the NCBI's FTP site! ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/003/195/GCA_000003195.3_Sorghum_bicolor_NCBIv3/ See: - https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#files Or "Access the data" on the right here: - https://www.ncbi.nlm.nih.gov ...
written 2.2 years ago by Dan500
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How to dump genes from GenBank in GFF3 format?
... If I look at this record in GenBank I see about 6k genes: https://www.ncbi.nlm.nih.gov/nuccore/CM000760?report=gbwithparts I'd really like to be able to dump those genes in GFF3 format, but I'm guessing I can't do that in a single step, so... 1. How to dump all genes from a GenBank record in 'wha ...
gff3 data-download genbank written 2.2 years ago by Dan500
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Comment: C: How to represent trans-spliced genes in GTF?
... Also, how to verify that the resulting GTF is valid? Compare the translation? ...
written 2.2 years ago by Dan500
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How to represent trans-spliced genes in GTF?
... For example, see this gene (nad1) in ENA: http://www.ebi.ac.uk/ena/data/view/ABI60879 If you look at the XML for that gene you see the following: join( DQ984518.1: 324706 .. 325091 , complement(DQ984518.1: 24417 .. 24498), complement(DQ984518.1: 22828 .. 23019) ...
gtf file-format trans-splicing written 2.2 years ago by Dan500 • updated 13 months ago by Biostar ♦♦ 20
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Answer: A: Where To Find Probe Sequences For Agilent Microarray?
... Ignore me, it's in a file called FASTA/015425_D_Fasta_20110210.txt (for example) in the design files .zip ...
written 2.5 years ago by Dan500
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Where To Find Probe Sequences For Agilent Microarray?
... Can't seem to find fasta files for common plant Agilent microarrays here: https://earray.chem.agilent.com/earray/ Anyone know how to get the fasta format probe sequences? ...
agilent archive array download written 2.5 years ago by Dan500
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Answer: A: Generate Consensus sequence from BAM file
... This question was already asked/answered here: https://www.biostars.org/p/126377/ If you still have errors, you should reword your question ;-) ...
written 2.6 years ago by Dan500
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How to download all UniGenes for a given species?
... Not sure if this question even makes sense... I'd like to get a complete set of UniGenes for a given species. When I search here: https://www.ncbi.nlm.nih.gov/unigene?term=4565%5BTaxonomy%20ID%5D What I get is a list of 178,464 'studies' (I guess) each containing its own list of UniGenes... Is ther ...
database unigene download written 2.6 years ago by Dan500
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What does ENA's "Data class" mean?
... Looking at an entry like this: http://www.ebi.ac.uk/ena/data/view/FJWB01000001 I see dataClass="WGS", but what does this mean? I can read a bit about it here: http://www.ebi.ac.uk/ena/submit/data-formats#ENA+data+classes But it really isn't clear what the difference between WGS, STD and CON. See ...
archive sequence submission ena written 3.0 years ago by Dan500

Latest awards to Dan

Student 17 months ago, asked a question with at least 3 up-votes. For Get number of variations in a huge VCF using Tabix?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Best Tool For Primer Design?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Formula For Converting Sequence To Physical Coverage
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Get number of variations in a huge VCF using Tabix?
Great Question 2.5 years ago, created a question with more than 5,000 views. For How To Find A 28Bp 'Primer' Sequence In A Genome?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Best Tool For Primer Design?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Get number of variations in a huge VCF using Tabix?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Retrieve GO terms for all completed genomes in GenBank
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Convert an 'intron-style' GFF3 file into an 'exon-style' GFF3 file
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Convert an 'intron-style' GFF3 file into an 'exon-style' GFF3 file
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How To Find A 28Bp 'Primer' Sequence In A Genome?
Supporter 3.8 years ago, voted at least 25 times.
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Publish Our Own Project
Popular Question 4.3 years ago, created a question with more than 1,000 views. For How To Find A 28Bp 'Primer' Sequence In A Genome?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For How To Find A 28Bp 'Primer' Sequence In A Genome?
Scholar 5.3 years ago, created an answer that has been accepted. For A: Retrieve GO terms for all completed genomes in GenBank
Teacher 6.5 years ago, created an answer with at least 3 up-votes. For A: Which Sequences Should I Include In A Whole Genome Alignment Of Primates?
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Publish Our Own Project
Popular Question 9.5 years ago, created a question with more than 1,000 views. For How To Find A 28Bp 'Primer' Sequence In A Genome?
Student 9.5 years ago, asked a question with at least 3 up-votes. For How To Find A 28Bp 'Primer' Sequence In A Genome?

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