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3
votes
2
answers
105
views
2
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Efetch extracting large fasta data from positon
efetch written 11 weeks ago by bengoaluoni • 0 • updated 11 weeks ago by Pierre Lindenbaum ♦ 129k
10
votes
4
answers
3.2k
views
6 follow
4
answers
Retrieve GFF3 file from ncbi
gff3 ncbi efetch written 2.5 years ago by john • 70 • updated 3 months ago by rohitsatyam102 • 170
1
vote
0
answers
165
views
0
answers
Get sequencing informations from NCBI with acc number
ncbi assembly efetch written 4 months ago by Chvatil • 40
5
votes
0
answers
205
views
0
answers
Catching error "QueryKey value not found in link output" when fetching taxonomy from NCBI
ncbi R efetch bash error_handling written 5 months ago by Freddy • 20 • updated 5 months ago by Asaf ♦ 8.3k
0
votes
1
answer
221
views
1
answer
efetch sra suddenly stopping
ncbi sra fastq esearch efetch written 7 months ago by barry • 0 • updated 7 months ago by ATpoint ♦ 36k
2
votes
1
answer
311
views
1
answer
Entrez Direct E-utilities on command line: efilter parameters for limiting efetch results
ncbi biosample efetch elink efilter written 8 months ago by sovrappensiero • 10 • updated 8 months ago by genomax ♦ 87k
1
vote
0
answers
210
views
0
answers
NCBI e-utilities: timeout and restart
ncbi esummary esearch efetch e-utilities written 9 months ago by joe • 140
4
votes
1
answer
884
views
6 follow
1
answer
How to extract gene ids from NCBI gene names using either efetch or python ?
ncbi efetch entrez written 15 months ago by lakhujanivijay ♦ 5.1k • updated 15 months ago by genomax ♦ 87k
1
vote
1
answer
816
views
1
answer
Entrez-efetch error. What could be wrong with my efetch usage?
sra-download efetch etrez-direct rna-seq written 15 months ago by jaqx008 • 70
2
votes
3
answers
4.1k
views
3
answers
Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
entrez direct e-utilities cds efetch retrieve written 3.9 years ago by al-ash • 140 • updated 16 months ago by Biostar ♦♦ 20
13
votes
3
answers
3.9k
views
11 follow
3
answers
efetch error LWP::Protocol::https not installed
efetch written 2.8 years ago by traviata • 10 • updated 17 months ago by indexofire • 30
0
votes
1
answer
3.0k
views
1
answer
Obtaining sequence from Bioproject IDs using biopython gives unknown sequence
efetch eutilities elink biopython written 5.2 years ago by Prasad • 30 • updated 17 months ago by Biostar ♦♦ 20
2
votes
2
answers
1.6k
views
5 follow
2
answers
web efetch Json out put which is not a real json
python efetch json biopython pubmed written 2.9 years ago by Lilizine • 0 • updated 18 months ago by MatthewP • 680
1
vote
1
answer
609
views
1
answer
Different output fields from efetch
python efetch sequence written 20 months ago by Medhat ♦ 8.7k • updated 20 months ago by Pierre Lindenbaum ♦ 129k
0
votes
1
answer
466
views
1
answer
Which tool to use to get all citations of a pmid paper?
entrez eutils efetch written 22 months ago by Saad Khan • 400 • updated 22 months ago by h.mon ♦ 30k
2
votes
1
answer
572
views
1
answer
Strand not working in biopython efetch
efetch biopython strand written 22 months ago by tim.ivanov.92 • 10 • updated 22 months ago by Joe ♦ 17k
2
votes
1
answer
1.8k
views
1
answer
Getting taxid from accession number
taxid efetch taxonomy genbank eutils written 2.3 years ago by auninsaw • 10
5
votes
3
answers
1.4k
views
3
answers
Cannot get efetch to download genome - what is wrong?
genome fasta efetch entrez written 2.3 years ago by BioBing • 120 • updated 2.3 years ago by h.mon ♦ 30k
0
votes
1
answer
966
views
1
answer
To get the name of the strains by searching assembly genome number GCF_
ncbi python efetch written 2.5 years ago by horsedog • 60 • updated 2.5 years ago by Joseph Hughes • 2.8k
3
votes
1
answer
1.6k
views
6 follow
1
answer
Fetching NCBI gene symbols from NCBI protein ids or GI identifiers
ncbi gene efetch entrez written 2.8 years ago by lakhujanivijay ♦ 5.1k • updated 2.8 years ago by Puli Chandramouli Reddy • 190
6
votes
1
answer
1.4k
views
1
answer
How to download all sequences of a list of proteins for a particular organism
entrez direct efetch esearch written 2.8 years ago by traviata • 10 • updated 2.8 years ago by Kevin Blighe ♦ 63k
0
votes
1
answer
743
views
1
answer
Nested loops write in xml
python loop biopython efetch xml written 2.9 years ago by Lilizine • 0
1
vote
1
answer
1.4k
views
1
answer
NCBI Entrez - efetch from PMC returns only abstract
efetch entrez pmc written 3.0 years ago by chaniart • 0 • updated 3.0 years ago by Jean-Karim Heriche ♦ 23k
10
votes
1
answer
3.8k
views
11 follow
1
answer
Download NCBI genomes using taxonomy id (taxid)
ncbi python efetch biopython written 3.4 years ago by David • 160 • updated 3.0 years ago by pedrorodrigues • 10
1
vote
0
answers
1.5k
views
0
answers
Entrez progammaticly: Direct efetch or epost + efetch
epost efetch entrez written 3.0 years ago by guedes.aureliano • 0
0
votes
1
answer
1.4k
views
1
answer
URL for NCBI Efetch + XML with full annotation table
ncbi xml efetch eutils annotation written 3.1 years ago by Pierre Lindenbaum ♦ 129k • updated 3.1 years ago by genomax ♦ 87k
2
votes
1
answer
956
views
1
answer
Mistakes in a bash script for adding taxid for nt database
taxid efetch nt database shell bash written 3.1 years ago by wyc661217 • 10 • updated 3.1 years ago by Istvan Albert ♦♦ 84k
0
votes
1
answer
1.4k
views
1
answer
Transfer GI to taxID by efetch in a loop
software error taxid efetch gi written 3.2 years ago by wyc661217 • 10
0
votes
1
answer
1.7k
views
1
answer
Using efetch(biopython) to get the fasta file of an mRNA, as well as the exon locations
python efetch biopython entrez written 3.2 years ago by Jacob • 10 • updated 3.2 years ago by Ben • 50
7
votes
1
answer
877
views
1
answer
Extract Bibliographic Reference from GEO dataset using EFetch?
geo ncbi efetch written 3.2 years ago by Tom • 30 • updated 3.2 years ago by Santosh Anand ♦ 5.1k
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