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Showing top results for tag: efetch • reset
1
vote
2
replies
259
views
How to download NCBI's Identical Protein Group (IPG) database
efetch IPG entrez NCBI
5 weeks ago by Peter • 0
0
votes
2
replies
384
views
Odd behaviour - NCBI Eutils
NCBI Eutils esearch Eutilities efetch
updated 7 months ago by 145k • written 7 months ago by • 0
2
votes
7
replies
1.0k
views
Selecting query format for repeated calls to NCBI's API
NCBI esummary elink API efetch
updated 6 months ago by 145k • written 7 months ago by 4.4k
3
votes
2
replies
599
views
Protein Sequence from Entrez by Taxonomic_ID: Very slow
Efetch entrez python protein sequence
11 months ago by The ▴ 180
7
votes
7
replies
1.6k
views
How to use efetch to download genome/proteome/etc. at the command line?
esearch ncbi efetch
updated 11 months ago by ▴ 160 • written 11 months ago by ▴ 380
0
votes
2
replies
699
views
efetch from NCBI E-utilities returns "curl error s 400 & 500" and takes a very long time
NCBI efetch E-utilities
13 months ago by Eugene • 0
4
votes
3
replies
1.4k
views
Getting species names and taxa id from assembly accession number
efetch biopython entrez
updated 16 months ago by ▴ 760 • written 16 months ago by ▴ 10
7
votes
6
replies
2.0k
views
Downloading bulk coding sequences from NCBI that include the organism name in the sequence header?
efetch edirect ncbi
updated 16 months ago by 145k • written 16 months ago by ▴ 20
0
votes
5
replies
944
views
Missing columns in meta table from SRA Selector
SRA esearch efetch
updated 17 months ago by 101k • written 17 months ago by • 0
10
votes
10
replies
1.7k
views
efetch problem on ARM Mac
efetch entrez-direct conda
18 months ago by frabomba6 ▴ 40
2
votes
2
replies
540
views
Problem using efetch -format acc, not the right accessions returned
efetch esearch edirect entrez
18 months ago by Lei ▴ 20
25
votes
11
replies
16k
views
10 follow
Retrieve GFF3 file from ncbi
gff3 ncbi efetch
updated 8 months ago by ▴ 760 • written 6.7 years ago by ▴ 130
0
votes
4
replies
1.1k
views
limit the number of efetch result
efetch EDirect.
22 months ago by tsutsui.data.analysis • 0
1
vote
1
reply
1.0k
views
Entrez.efetch with retmax=1000000 not retrieving more than 10000 records (python)
python entrez efetch
updated 2.1 years ago by 145k • written 2.1 years ago by • 0
2
votes
7
replies
1.4k
views
headers missing in efetch results for SRA database
SRA Entrez.Direct efetch
updated 2.2 years ago by ▴ 510 • written 2.2 years ago by ▴ 90
4
votes
2
replies
802
views
retrieve all nt sequences for a taxid list
ncbi taxid efetch
updated 2.3 years ago by 145k • written 2.3 years ago by ▴ 10
6
votes
3
replies
1.5k
views
How to download a large number of protein.faa.gz files from NCBI's FTP site in one go
NCBI entrez FTP efetch
2.3 years ago by beginner123 ▴ 30
2
votes
2
replies
718
views
unexpected output from efetch
efetch
2.6 years ago by andres.firrincieli 3.7k
1
vote
3
replies
1.1k
views
How to use efetch to download specific gene from whole genome NCBI by linux terminal?
efetch NCBI terminal
2.6 years ago by Ahmad ▴ 10
1
vote
2
replies
1.6k
views
pubmed's esearch does not return a result though the searched title/publication do exists
efetch mesh pubmed esearch retrieval information
2.6 years ago by mehmet ali • 0
2
votes
3
replies
2.6k
views
NCBI's Efetch not working
edirect efetch
2.8 years ago by Jonathan ▴ 20
2
votes
5
replies
2.3k
views
switch off warning in blast command line
efetch ensembl warnings
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 710
0
votes
1
reply
793
views
Export ensembl efetch in comma-delimited format
format efetch ensembl
updated 3.4 years ago by 145k • written 3.4 years ago by ▴ 710
0
votes
0
replies
608
views
Best way for finding annotated counterparts of unknown transcript after BLAST
blast efetch pipeline annotation
3.5 years ago by Mathias • 0
2
votes
7
replies
1.6k
views
NCBI eutils EFETCH only fetch elements needed (or remove abstract from response)?
efetch eutils API pubmed ncbi
3.6 years ago by chaitanya.bangera ▴ 10
2
votes
4
replies
1.1k
views
bash find consecutive acc. no. & insert text
bash NCBI efetch
updated 18 months ago by 44k • written 3.7 years ago by ▴ 30
4
votes
2
replies
3.4k
views
downloading full genbank file using Entrez efetch
genbank full genbank entrez efetch
updated 3.8 years ago by ★ 3.7k • written 3.8 years ago by ▴ 40
5
votes
6
replies
2.7k
views
Joining multiple query keys in entrez Efetch
entrez Efetch biopython NCBI
3.9 years ago by timothy.kirkwood ▴ 140
0
votes
0
replies
691
views
efetch results incomplete
ncbi E-utility esearch efetch entrez
4.0 years ago by j.j.e.vanhooff • 0
1
vote
1
reply
835
views
Retrieve all annotated features in a GenBank record
efetch edirect genbank feature annotations
4.1 years ago by al-ash ▴ 210
4
votes
6
replies
8.7k
views
Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
Entrez Direct E-utilities efetch CDS retrieve
4.1 years ago by al-ash ▴ 210
0
votes
1
reply
1.0k
views
how to download all reference files with ensembl and taxon ID?
sequence ensembl efetch esearch
4.1 years ago by marongiu.luigi ▴ 710
3
votes
4
replies
783
views
Efetch extracting large fasta data from positon
Efetch
updated 4.4 years ago by 164k • written 4.4 years ago by • 0
1
vote
4
replies
908
views
Get sequencing informations from NCBI with acc number
ncbi Assembly efetch
4.5 years ago by Chvatil ▴ 130
5
votes
3
replies
1.3k
views
Catching error "QueryKey value not found in link output" when fetching taxonomy from NCBI
NCBI r efetch bash error_handling
updated 4.6 years ago by 10k • written 4.6 years ago by ▴ 60
0
votes
2
replies
876
views
efetch sra suddenly stopping
fastq sra ncbi efetch esearch
updated 4.7 years ago by 84k • written 4.7 years ago by • 0
2
votes
7
replies
1.9k
views
Entrez Direct E-utilities on command line: efilter parameters for limiting efetch results
ncbi efilter efetch elink biosample
updated 4.9 years ago by 145k • written 4.9 years ago by ▴ 100
1
vote
3
replies
1.3k
views
NCBI e-utilities: timeout and restart
NCBI esearch esummary efetch E-utilities
4.9 years ago by noodle ▴ 590
4
votes
1
reply
3.4k
views
How to extract gene ids from NCBI gene names using either efetch or python ?
ncbi entrez efetch
updated 5.4 years ago by 145k • written 5.4 years ago by 5.9k
1
vote
6
replies
3.4k
views
Entrez-efetch error. What could be wrong with my efetch usage?
efetch RNA-Seq Entrez-direct
updated 18 months ago by 44k • written 5.4 years ago by ▴ 110
14
votes
8
replies
8.1k
views
7 follow
efetch error LWP::Protocol::https not installed
efetch
updated 5.6 years ago by ▴ 40 • written 7.0 years ago by ▴ 20
0
votes
3
replies
4.3k
views
Obtaining sequence from Bioproject IDs using biopython gives unknown sequence
efetch elink biopython eutilities
updated 21 months ago by 44k • written 9.3 years ago by ▴ 50
4
votes
7
replies
4.5k
views
web efetch Json out put which is not a real json
json efetch biopython python pubmed
updated 5.7 years ago by ★ 1.4k • written 7.1 years ago by ▴ 10
1
vote
3
replies
2.0k
views
Different output fields from efetch
python sequence efetch
updated 5.8 years ago by 164k • written 5.8 years ago by 9.8k
0
votes
1
reply
1.4k
views
Which tool to use to get all citations of a pmid paper?
entrez eutils efetch
updated 6.0 years ago by 35k • written 6.0 years ago by ▴ 440
2
votes
3
replies
1.7k
views
Strand not working in biopython efetch
biopython efetch strand
updated 6.0 years ago by 21k • written 6.0 years ago by ▴ 40
2
votes
3
replies
5.9k
views
Getting taxid from accession number
taxid taxonomy genbank eutils efetch
6.4 years ago by auninsaw ▴ 10
7
votes
7
replies
3.8k
views
Cannot get efetch to download genome - what is wrong?
entrez genome efetch fasta
updated 6.5 years ago by 35k • written 6.5 years ago by ▴ 150
2
votes
3
replies
2.2k
views
To get the name of the strains by searching assembly genome number GCF_
NCBI efetch python
updated 6.7 years ago by ★ 3.0k • written 6.7 years ago by ▴ 60
4
votes
6
replies
3.1k
views
Fetching NCBI gene symbols from NCBI protein ids or GI identifiers
efetch NCBI entrez gene
updated 6.9 years ago by ▴ 190 • written 6.9 years ago by 5.9k
50 results • Page 1 of 1
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It has been moved to a comment (looks like you are a moderator that seems to have come back after a long break). You can accept @dgtool ans…
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For trios and short-reads, I use delly or manta to get a join VCF of the trio (+ a few controls to discard false positives). I then kee…
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Thank you your suggestion on using -O worked. Makes sense in hind-sight. Sorry I couldn't select your answer as the "winner" as you poste…
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OK, so as far as I understand "mendelian precision" is "just" looking at the de-novo CNVs....
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In the paper HadoopCNV(Yang H, Chen G, Lima L, Fang H, Jimenez L, Li M, Lyon GJ, He M, Wang K. HadoopCNV: A dynamic programming imputation …
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Hi, thank you for your attention. Here is my dataframe as you asked structure(list(Pathway = c("Alpha-amino acid biosynthetic proc. ",…
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>"using mendelian precision" what do you mean ?
Comment: Pedigree information by heureuse • 0
That was the question. Thank you for the answer. It helps.
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