User: vkkodali

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vkkodali1.1k
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Posts by vkkodali

<prev • 116 results • page 2 of 12 • next >
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Comment: C: Change NBCI accession numbers to UNIPROT identifiers
... For programmatic mapping of IDs, you can use UniProt's REST API as described here: https://www.uniprot.org/help/api_idmapping ...
written 8 weeks ago by vkkodali1.1k
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Comment: C: Number of discovered genes in genome does not correspond with published annotati
... > It extract 3 column of gff file No it doesn't. Please make sure your code works as intended before posting. Even if it did, it will count the number of, for example, CDS lines in the GFF3 file which will be wildly off the actual number. That's because a given gene can have many alternately s ...
written 8 weeks ago by vkkodali1.1k
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Comment: C: Number of discovered genes in genome does not correspond with published annotati
... What is this supposed to do? Please explain. ...
written 8 weeks ago by vkkodali1.1k
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Answer: A: Number of discovered genes in genome does not correspond with published annotati
... You are counting the wrong column. Try this instead. $ zgrep -v '^#' GCF_003368295.1_ASM336829v1_genomic.gff.gz \ | awk 'BEGIN{FS="\t";OFS="\t"}($3=="CDS"){print $9}' \ | grep -Po 'GeneID:\d+' \ | sort -u \ | wc -l 53614 Apparently, there are a bunch of CDS ...
written 8 weeks ago by vkkodali1.1k
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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 9 weeks ago by vkkodali1.1k
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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 9 weeks ago by vkkodali1.1k
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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 9 weeks ago by vkkodali1.1k
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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 9 weeks ago by vkkodali1.1k
0
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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 10 weeks ago by vkkodali1.1k
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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 12 weeks ago by vkkodali1.1k

Latest awards to vkkodali

Teacher 18 days 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 23 days ago, received more than 100 upvotes.
Commentator 28 days ago, created a comment with at least 3 up-votes. For C: Change NBCI accession numbers to UNIPROT identifiers
Centurion 9 weeks ago, created 100 posts.
Scholar 12 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 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: 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 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?
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?
Scholar 5 months ago, created an answer that has been accepted. For C: Strange esearch behavior
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?
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?

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