User: vkkodali

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vkkodali1.3k
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Posts by vkkodali

<prev • 154 results • page 1 of 16 • next >
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Comment: C: NCBI e-utilities: timeout and restart
... Is this your real query or just something that you picked as an example? Something is not right... it returns 127 million hits for this query which I think is pretty much the entire Protein database. If you search for the term `CRISPR` in the [NCBI Protein portal](https://www.ncbi.nlm.nih.gov/protei ...
written 1 day ago by vkkodali1.3k
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Comment: C: How to obtain all accession.version identifiers for a BLAST database using ENTRE
... For a given `db`, you can find all available link names and a brief description as follows: einfo -db blastdbinfo The [Entrex Link Descriptions](bit.ly/elink-descriptions) webpage also lists this information but I am not sure how up-to-date that is. It looks like `blastdbcmd` may be the best ...
written 3 days ago by vkkodali1.3k
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Answer: C: XML from entrez not formatted correctly
... This appears to be unnecessarily complicated to me. For a given list of SRA accessions, you should be able to just download the comma-separated runinfo table from the command line (without going through R) and then parse the output file as a CSV from within R. Do you need to do everything from withi ...
written 6 days ago by vkkodali1.3k
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Comment: C: XML from entrez not formatted correctly
... Good eyes! It was my (and the OP's) mistake. You see we both used `-target sra` for our target db in the elink. So, the data that was being fetched was for the identifier `561398` from SRA instead of BioProject. I now fixed my command to use `-target bioproject` to get the correct data out. ...
written 6 days ago by vkkodali1.3k
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Comment: C: Gene names from gene ids for Pisum Sativum
... Can you please further elaborate on how you got the annotation? Perhaps give a few examples of gene_id, tracking_id and locus_id? ...
written 6 days ago by vkkodali1.3k
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Comment: C: XML from entrez not formatted correctly
... > I think this bit in the original post does not match information I obtained when using runinfo Is that not expected? Your command is fetching the `runinfo` table whereas @joe was downloading the Bioproject docsum. The corresponding edirect command for what @joe was doing: esearch -db sra ...
written 6 days ago by vkkodali1.3k
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Comment: C: XML from entrez not formatted correctly
... > it's also the data returned is incorrect Could you please explain what data are incorrect? ...
written 6 days ago by vkkodali1.3k
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Comment: C: NCBI vs Liftover vs ENSEMBL for Assembly Conversion for SNP data (GRCh37 to GRCh
... In that case then you should be using `GRCh37.p13 :: Primary Assembly` as the source assembly and `GRCh38.p13 :: Primary Assembly` as the target. Are these not working for you? Do you see instances of misplacement? I expect at least some differences between UCSC, NCBI and Ensembl considering the ...
written 7 days ago by vkkodali1.3k
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Comment: C: NCBI vs Liftover vs ENSEMBL for Assembly Conversion for SNP data (GRCh37 to GRCh
... I cannot speak for the Ensembl or UCSC alignments but for NCBI, using the correct query and target assemblies is very important. Does your GRCh37 data include SNPs on the Primary Assembly (chromosomes + unlocalized + unplaced scaffolds) or more? A quick way to check this would be to just generate a ...
written 10 days ago by vkkodali1.3k
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Answer: A: NCBI rRNA sequence search
... When you are searching for 'Drosophila melaogaster genome' and then going to the 'Nucleotide' portal you are likely looking at RefSeq sequences only. On the other hand, if you search for 'Drosophila melanogaster' in the Nucleotide portal, both GenBank and RefSeq sequences are returned. One of the fi ...
written 18 days ago by vkkodali1.3k

Latest awards to vkkodali

Scholar 6 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 14 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 10 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 5 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 5 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Guru 7 months ago, received more than 100 upvotes.
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Change NBCI accession numbers to UNIPROT identifiers
Centurion 9 months ago, created 100 posts.
Scholar 9 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 10 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 10 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 10 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?

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