User: vkkodali

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vkkodali910
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910
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5 hours ago
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2 years, 6 months ago
Email:
v*****@gmail.com

Posts by vkkodali

<prev • 102 results • page 1 of 11 • next >
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Answer: A: Number of genomes sequences in NCBI
... If all you are after is a count (and not particularly interested in downloading the assemblies), you can do this from the NCBI Assembly web portal. This way, you won't have to bother downloading and installing a couple of other programs on your machine if you don't want to. 1. Search for the foll ...
written 4 days ago by vkkodali910
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Comment: C: How can I parse a json file from MobiDB to retrieve proteome data?
... I doubt they ever had the files in json format. At least when I wrote the script shown below, the files were in mjson format (see Usage portion below; the filename as mjson in it). ...
written 4 days ago by vkkodali910
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Comment: C: Number of genomes sequences in NCBI
... RefSeq assembly_summary.txt files for broad categories such as vertebrate_mammalian are present in corresponding directories in this path: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/ For example, the assembly_summary.txt file for the vertebrate_mammalian is here: ftp://ftp.ncbi.nlm.nih.gov/genomes/r ...
written 5 days ago by vkkodali910
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Comment: C: CLINVAR multiple molecular consequences
... Each one of those NM and NR accessions appear to be alternate splice variants encoded by the gene HACE1. Depending on the coding sequence, and where it ends up in that particular alt splice variant, the consequence can be different. In the case of NM_020771.3, a C>T mutation would result in a ter ...
written 6 days ago by vkkodali910
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Comment: C: Avoid download limit from NCBI entrez with Biopython using API key
... Could you please post your entire query? The API key applies only to records fetched using eUtilities. If your ultimate goal is download genome sequence data, you should use FTP instead. If you can provide more information about what you are trying to download and the query you are using, I will be ...
written 11 days ago by vkkodali910
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Answer: A: Downloading individual reads from SRA
... You can probably use `fastq-dump` to download SRR1803613.479767.1 as follows but I haven't tried paired reads, etc with this. fastq-dump -A SRR1803613 -N 479767 -X 479767 --fasta ...
written 27 days ago by vkkodali910
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Comment: C: GenBank features don't extract sequences based on condition Biopython
... Fair enough. Just for the sake of others who may end up here at a later point in time, one can use Biopython to query Entrez databases, get the FTP path, download the feature table file, parse it using Python and then use Biopython Entrez to download the FASTA sequences (see http://biopython.org/DI ...
written 4 weeks ago by vkkodali910
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Comment: C: GenBank features don't extract sequences based on condition Biopython
... I do realize that you will be doing this on multiple genomes. If anything, this will save you some disk space too because instead of downloading entire genomes in genbank flat file format, you will have to download the much smaller feature_table.txt.gz files. If you have a list of assembly accessi ...
written 4 weeks ago by vkkodali910
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Answer: A: GenBank features don't extract sequences based on condition Biopython
... You can use the `feature_table.txt` file in combination with `efetch` tool from [Entrez Direct](bit.ly/entrez-direct) as shown below. A feature table file for every annotated assembly is present in the FTP location from where you may have downloaded the genome genbank flat files from. For example, ...
written 4 weeks ago by vkkodali910
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Comment: C: Programmatic access to Sample Information from GEO via GSM or SRR number
... If you are planning to write a loop, be sure to check out the sections on While Loop and For Loop here: https://www.ncbi.nlm.nih.gov/books/NBK179288/#chapter6.Automation ...
written 5 weeks ago by vkkodali910

Latest awards to vkkodali

Centurion 4 days ago, created 100 posts.
Scholar 27 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 5 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 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 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?
Teacher 5 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 8 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 9 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?
Teacher 9 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 9 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?
Teacher 9 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 9 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?
Teacher 10 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?
Teacher 11 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 3 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 3 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 3 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 3 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 3 months ago, created an answer that has been accepted. For C: Strange esearch behavior
Teacher 3 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 3 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 3 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 3 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 3 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 3 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?

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