User: piet

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piet1.4k
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Posts by piet

<prev • 189 results • page 1 of 19 • next >
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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 13 days 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 17 days 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 23 days 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 25 days 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 25 days 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 26 days 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 4 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 4 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 4 months ago by piet1.4k
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Comment: C: How can I check the direction of DNA replication?
... The replication complex is a huge protein machinery. It moves from ORI to TER. During its move, both strands are replicated. This is complicated since the mechanisms for the leading and the lagging strand are totally different. However, the overall move of the whole replication apparatus (sometimes ...
written 4 months ago by piet1.4k

Latest awards to piet

Teacher 25 days 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 25 days ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Appreciated 6 months ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
Popular Question 6 months ago, created a question with more than 1,000 views. For Howto use NCBI programs behind a HTTP proxy
Supporter 14 months ago, voted at least 25 times.
Teacher 15 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 16 months ago, received more than 100 upvotes.
Teacher 17 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 17 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Centurion 18 months ago, created 100 posts.
Teacher 18 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 19 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 20 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
Appreciated 21 months ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
Scholar 21 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 21 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
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Python Programming (Suggestions are needed)
Scholar 21 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 21 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 21 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 2.1 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 2.4 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 3.1 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

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