User: rororo

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rororo0
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Posts by rororo

<prev • 27 results • page 1 of 3 • next >
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Get genomes in genbank that are NOT in RefSeq
... NCBI has two sections for assemblies, genbank (all submitted sequences) and RefSeq (curated genbank sequences). A list of both is available here: ```ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt ``` and ```ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.t ...
genome ncbi refseq genbank written 7 months ago by rororo0 • updated 7 months ago by vkkodali2.0k
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Comment: C: Gff to genbank - feature is missing
... this is the script I posted above ...
written 24 months ago by rororo0
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Comment: C: Gff to genbank - feature is missing
... as soon as the 25,000 entries are read and returned, seqret starts from the beginning and returns the same sequences again and again ...
written 24 months ago by rororo0
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Comment: C: Gff to genbank - feature is missing
... thanks for your help. Unfortunately, seqret does not stop converting - the file just gets bigger and bigger. Artemis freezes when opening the gff-file ...
written 24 months ago by rororo0
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Comment: C: Gff to genbank - feature is missing
... sorry, I clearified the source! ...
written 24 months ago by rororo0
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Comment: A: Gff to genbank - feature is missing
... I have 25,000 entries. So I need an automatic way! ...
written 24 months ago by rororo0
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Comment: C: Gff to genbank - feature is missing
... `source` in the `FEATURES` table FEATURES Location/Qualifiers source 1..5028 /organism="Saccharomyces cerevisiae" /db_xref="taxon:4932" /chromosome="IX" /map="9" ...
written 24 months ago by rororo0
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Gff to genbank - feature is missing
... I want to predict genes from my organism of interest using `augustus`. I therefore have my assembly, as well as a gff3 file. I want to train augustus using my dataset using `etraining`. I therefore need a genbank file. I found [link][1] with the following script to convert gff+fasta to genbank, sin ...
gff3 augustus dna genbank bioinformatics written 24 months ago by rororo0 • updated 22 months ago by Biostar ♦♦ 20
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Microscope/Genoscope RESTful API
... Does anyone know how to download ('export') all files from one organism on the Microscope/Genoscope platform? They offer a REST API interface but there is no manual. this is how the site (for whatever organism is chosen) looks like: https://www.genoscope.cns.fr/agc/microscope/search/exportForm.php? ...
rest genoscope api databases mage written 2.1 years ago by rororo0
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Comment: C: SRAdb: Search full text in study_type
... NCBI does not mention SRA ...
written 2.2 years ago by rororo0

Latest awards to rororo

Great Question 15 months ago, created a question with more than 5,000 views. For Tool for calculating sequence statistic values (e.g. N50) for multiple bins
Popular Question 15 months ago, created a question with more than 1,000 views. For List of all GO terms
Popular Question 15 months ago, created a question with more than 1,000 views. For Tool for calculating sequence statistic values (e.g. N50) for multiple bins
Popular Question 23 months ago, created a question with more than 1,000 views. For List of all GO terms
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Tool for calculating sequence statistic values (e.g. N50) for multiple bins

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