Questions tagged [ncbi]
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Facing problem with BLASTx using BioPython in Google Colab
I'm trying to BLASTX a sequence using Biopython in Google Colab. Here is the code I am using. I'm not able to understand why I am getting an empty list [] for ...
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How to annotate Agilent probeIDs and obtain corresponding RefSeqmRNA from NCBI in a microarray analysis in R?
I am working on a microarray analysis using Agilent data (SurePrint G3 Mouse GE 8x60K IDs e.g. A_30_P01020727), having the list of Probe IDs with it´s corresponding statistics and fold changes. My ...
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Where can I get hg38 Copy number Variation (CNV) file?
I'm wondering how can I get standard hg38 Copy number Variation (CNV) file from UCSC website.
Although, I got a link that is not working: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/...
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Liftover variants/vcf called on NCBI reference genome
I have been tackling this problem for a while now, and I hope someone has a better answer.
I need to liftover variants (.vcf) from NCBI hg37 to NCBI hg38. The NCBI remapping tool has been depreciated. ...
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How can I download multiple SRR* files at a time when using sratoolkit's fastq-dump?
I have multiple SRR files to download, and their accession is in a list:
SRR9004325
SRR9004326
SRR9004327
I read the NCBI document but don't find how to achieve ...
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arm64 installation of AMRFinderPlus
I was trying to install NCBI AMRFinderPLUS on my Nvidia Jetson using standard Bioconda based installtion. However, all the time it is giving error that the package is not available and I thought I am ...
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What does this BLASTN mean: Error pre-fetching sequence data?
I am trying to run BLASTN on a 14GB Pseudomonas database using the command: blastn -db ~/pseudomonas-db/pseudomonas -query ~/desktop/inputfiles/poz176.fasta -out poz176-out -num_threads 8
I get the ...
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getting NCBI TAXname by R
I have a data frame on R, called qIns8, with 14 columns and 204 rows. the column called "subject tax id" has NCBI taxIDs for the corresponding row, I need a script to add another column to ...
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How can I limit blast results to exclude a specific taxonomic ID?
I would like to perform blast+, using the command line, here is the code:
-task blastn -db nr -outfmt 7 -query myQuery.fas -out result.txt -remote.
I have to ...
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error in downloading the annotation of sequences on NCBI
I have developed an R function to download the "organism" name of the numerous NCBI accession numbers which are already saved in an object.
The function:
...
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86
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How to BLAST a protein against a large set of organisms?
I have a list of organisms with their full scientific names and Taxonomy IDs, total ~1500. I want to BLAST my protein against this 1500 genome or proteome. How can I do that?
Here a sample protein ...
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196
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Shell script to validate fastq issue
I have two GSM ID as test case where both of them are having data when I checked through sra explorer tool but when I try to fetch through a script only one of them returns output where the other one ...
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Linking GenBank records to biosamples (and vice versa) using edirect
Assume that I wish to find all complete human mitochondrial genome records on GenBank (or rather, NCBI nuccore) that also have an entry in NCBI's Biosample database.
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86
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Get SRR numbers from a GSE number
I'm trying to programmatically download files from SRA (with prefetch in sra-tools) starting from a GSE number, using Python.
There is an explanation for using entrez-direct on the CLI, using esearch ...
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410
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ncbi fastq dump error in loop
I have a very basic objective which I want to give list of id to a ncbi-srafastq tool kit which will prefetch the id which is in .sra file extension and then it will run fastq-dump on the file to ...
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