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3 votes

Where can I get hg38 Copy number Variation (CNV) file?

If you want databases of known CNVs, you can have a look at: Database of Genomic Variants (DGV) DECIPHER NIH GTEx Clinvar CNV NCBI dbVar You can also use VarSome, a free genomic variant search ...
terdon's user avatar
  • 10.2k
3 votes
Accepted

What is the NCBI's definition of an "atypical genome"?

Biostars user MirianT_NCBI provided an answer on my crosspost, which I'm copying here: You can find more information about what constitute an atypical genome in this FAQ. Here's the list of reasons ...
acvill's user avatar
  • 613
3 votes
Accepted

NCBI Blast databases - cannot find some databases

I don't think there is a human_nr or human_nt database for NCBI. An equivalent database is accessible via the standard nr/nt database and simply restrict the ...
M__'s user avatar
  • 12.6k
3 votes
Accepted

ncbi fastq dump error in loop

The main problem is that your script is inadvertently treating a set of file and directory names as a single SRA accession number, all in one variable. You should update it to work with each ...
Jesse's user avatar
  • 947
2 votes

getting NCBI TAXname by R

I developed the function and it worked perfectly, ...
Farzad Beikpour's user avatar
2 votes

Shell script to validate fastq issue

Use the SRR accessions, not the sample-IDs you are using. With entrez e-utils, I found the SRR of GSM2683458: ...
user3479780's user avatar
2 votes

How important are the homozygous variants that get unnecessarily deleted using liftover?

All this is saying is that the tool doesn't lift over variants which aren't present in the vcf. I can't imagine this being a big deal in any analysis I've done and it's exactly what I'd expect the ...
user438383's user avatar
  • 1,689
2 votes

How can I download multiple SRR* files at a time when using sratoolkit's fastq-dump?

If fasterq-dump can't read from a file, you can simply loop over the file yourself: ...
terdon's user avatar
  • 10.2k
1 vote

Where can I get hg38 Copy number Variation (CNV) file?

Thanks for all the responses, I found one database that caters standard CNVs of hg38 as well as other versions. Although, I've to confirm which dataset will going to work for me. Please let me know if ...
Deb's user avatar
  • 289
1 vote

Liftover variants/vcf called on NCBI reference genome

Could you use the hg19 --> hg38 chain from here? As I understand it, the main difference between GrCH37 and hg19 are the format the chromosomes are written (whether there is a "chr" ...
Sarah's user avatar
  • 516
1 vote

Liftover variants/vcf called on NCBI reference genome

Liftover is hard. While many variants can be lifted over relatively easily, some cannot. First, some variants are not even variants in the other genome (the other genome has the variant allele as the ...
terdon's user avatar
  • 10.2k
1 vote

arm64 installation of AMRFinderPlus

Try the following conda install bioconda::ncbi-amrfinderplus The above does work I tested it (below). There could be an issue with you version of conda (24.1.2 OSX)...
M__'s user avatar
  • 12.6k
1 vote

What does this BLASTN mean: Error pre-fetching sequence data?

Based on other posts elsewhere it seems likely that there is something funky about your database. How did you generate it? Could you try to re-generate the db without the ...
Maximilian Press's user avatar
1 vote

How can I limit blast results to exclude a specific taxonomic ID?

This isn't particularly elegant, but it should work. First, extract the accessions into a file. Next, get the taxid for each of the accessions. Once you have that, you can identify the accessions that ...
terdon's user avatar
  • 10.2k
1 vote

error in downloading the annotation of sequences on NCBI

You could use the tryCatch function to handle inputs that throw an error. A good example on how to write them can be found here. Though the message indicates it's a ...
dthorbur's user avatar
  • 121
1 vote
Accepted

How to BLAST a protein against a large set of organisms?

My solution is simply. perform a web-based Blastp using the following parameters: most dissimilar 5000 hits (maximum limit) Restrict to Archaea (which is what you samples appear to be)* If you hit ...
M__'s user avatar
  • 12.6k
1 vote

How to BLAST a protein against a large set of organisms?

In the interface of blastp, you can limit the search space to organisms you want to. Yo can do this by introducing name species or Tax IDs, you can add more than one, but I bet you don't wanna ...
JRodrigoF's user avatar
  • 827
1 vote

Reference genome (bwa -mem)

What you need is the genome sequence in fasta format, typically suffixed .fa, for example from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/ This ...
ATpoint's user avatar
  • 1,430
1 vote

ZIP the fasterq-dump files in loop

I tried this and it worked ...
Shradha Sharma's user avatar
1 vote

ZIP the fasterq-dump files in loop

Haven't tried, but I believe you may add -Z to fasterq-dump and remove -k ${i} from gzip. In addition, I would recommend the ...
user172818's user avatar
  • 6,545
1 vote
Accepted

How to get the nucleotide sequence for protein NCBI accession code, programatically?

Yes its easy using Biopython. What I'm requesting is the sequence must be >9500 otherwise it's discarded. In your case this value will be MUCH bigger, because these are bacterial genomes. ...
M__'s user avatar
  • 12.6k
1 vote
Accepted

How do i search by these gene properties in NCBI's GenBank?

This can be done using the NCBI eutils command-line tools. For taxa, the correct incantation for the search string is txid<taxID>[Organism] (assuming you want ...
gringer's user avatar
  • 14.4k
1 vote

Kraken2 Standard Database failing to build (unexpected FTP path)

I have experienced the same issue yesterday and after trying the --use-ftp argument without luck (this is proposed as an alternative in the forums), I have ...
haci's user avatar
  • 4,162
1 vote
Accepted

How to set Entrez Direct - ESearch NCBI entrez to pipe or ignore errors?

This is because there are not assemblies for Crepis commutate within NCBI's assembly database. The cross check is here: https://www.ncbi.nlm.nih.gov/assembly/?term=Crepis+commutata The output is a bit ...
M__'s user avatar
  • 12.6k

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