User: piet

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piet1.4k
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Posts by piet

<prev • 190 results • page 1 of 19 • next >
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Answer: A: Insert size on PE 2*250
... In most cases these libraries with average insert size much smaller than read length assemble well for most part of bacterial genomes. But it is a hugh wast of effort, with most of your fragments you will sequence a long tail of nonsense. And you will loose the ability to assemble accross some (shor ...
written 3 months ago by piet1.4k
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Comment: C: Physical/Fragment Coverage for Paired-Ends: Read Length
... Does "N_reads" represents the number of reads or the number of fragments/spots that were sequenced? ...
written 6 months ago by piet1.4k
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Comment: C: NCBI : New API Keys for the E-utilities
... Using Eutils has never been an easy exercise, nor will it be in future. ...
written 6 months ago by piet1.4k
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... I did not know about the JSON, that is interesting. ...
written 6 months ago by piet1.4k
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Comment: C: How to download sample attributes (sample metadata) file from the European nucle
... Are you behind a HTTP proxy? ...
written 6 months ago by piet1.4k
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Answer: A: How to download sample attributes (sample metadata) file from the European nucle
... > Unfortunately NCBI does not contain metadata for this project. This is not true. You can easily download a XML file containing all of the attributes of all the biosamples from NCBI. Since the procedure may also be useful in other contexts, I will describe it step by step. First go to the pag ...
written 6 months ago by piet1.4k
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Answer: A: How to download sample attributes (sample metadata) file from the European nucle
... I my opinion, NCBI Entrez/Eutils is more versatile than EBI for downloads like this. If you want to stick with EBI, you can run the loop over all entries of the project on your local computer. There are only 147 samples. Since tasks like this are usually run only once, do not worry to much about com ...
written 6 months ago by piet1.4k
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Answer: A: How to automatically find the right species name when there are typos, using Ent
... You can download a dump of the taxonomy database from NCBI, it is updated several times a day. ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz There is also a REDME file which explains the format of the ASCII files contained in the TAR ball. ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_ ...
written 10 months ago by piet1.4k
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Comment: C: do blast search using gi numbers
... NCBI is hiding GI numbers from inexperienced kids now, but you can still use them in blast queries and eutils. (see below) ...
written 10 months ago by piet1.4k
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Answer: A: do blast search using gi numbers
... I do not have the cog database installed on my machine, but some tests with blastp instead of rpsblast indicate, that it is neccessary to put every GI number in a separate line: echo 'gi|292833481\ngi|383341230\n' | blastp -task blastp-fast -remote -db nr -outfmt 6 The above command will emit ...
written 10 months ago by piet1.4k

Latest awards to piet

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Scholar 6 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Appreciated 12 months ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
Popular Question 12 months ago, created a question with more than 1,000 views. For Howto use NCBI programs behind a HTTP proxy
Supporter 20 months ago, voted at least 25 times.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Guru 22 months ago, received more than 100 upvotes.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Scholar 24 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Centurion 24 months ago, created 100 posts.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
Scholar 2.3 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Python Programming (Suggestions are needed)
Scholar 2.3 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Scholar 2.3 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 2.6 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 2.9 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species

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