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4
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296
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6 follow
1
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How to extract gene ids from NCBI gene names using either efetch or python ?
ncbi efetch entrez written 5 months ago by lakhujanivijay ♦ 4.5k • updated 5 months ago by genomax ♦ 73k
1
vote
1
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339
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1
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Entrez-efetch error. What could be wrong with my efetch usage?
sra-download efetch etrez-direct rna-seq written 6 months ago by jaqx008 • 60
2
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3
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3.3k
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3
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Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
entrez direct e-utilities cds efetch retrieve written 3.1 years ago by al-ash • 110 • updated 6 months ago by Biostar ♦♦ 20
13
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3
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2.9k
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11 follow
3
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efetch error LWP::Protocol::https not installed
efetch written 2.1 years ago by traviata • 10 • updated 7 months ago by indexofire • 30
0
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1
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2.6k
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1
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Obtaining sequence from Bioproject IDs using biopython gives unknown sequence
efetch eutilities elink biopython written 4.4 years ago by Prasad • 10 • updated 7 months ago by Biostar ♦♦ 20
0
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2
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1.2k
views
2
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web efetch Json out put which is not a real json
python efetch json biopython pubmed written 2.1 years ago by Lilizine • 0 • updated 8 months ago by MatthewP • 260
1
vote
1
answer
374
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1
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Different output fields from efetch
python efetch sequence written 10 months ago by Medhat ♦ 8.5k • updated 10 months ago by Pierre Lindenbaum ♦ 123k
0
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1
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318
views
1
answer
Which tool to use to get all citations of a pmid paper?
entrez eutils efetch written 12 months ago by Saad Khan • 370 • updated 12 months ago by h.mon ♦ 27k
2
votes
1
answer
383
views
1
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Strand not working in biopython efetch
efetch biopython strand written 13 months ago by tim.ivanov.92 • 10 • updated 13 months ago by Joe ♦ 14k
2
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1
answer
1.0k
views
1
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Getting taxid from accession number
taxid efetch taxonomy genbank eutils written 18 months ago by auninsaw • 10
7
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3
answers
2.0k
views
3
answers
Retrieve GFF3 file from ncbi
gff3 ncbi efetch written 20 months ago by john • 70 • updated 18 months ago by ucpete • 20
5
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3
answers
906
views
3
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Cannot get efetch to download genome - what is wrong?
genome fasta efetch entrez written 18 months ago by BioBing • 100 • updated 18 months ago by h.mon ♦ 27k
0
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1
answer
703
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1
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To get the name of the strains by searching assembly genome number GCF_
ncbi python efetch written 21 months ago by horsedog • 50 • updated 21 months ago by Joseph Hughes • 2.7k
3
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1
answer
1.3k
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6 follow
1
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Fetching NCBI gene symbols from NCBI protein ids or GI identifiers
ncbi gene efetch entrez written 23 months ago by lakhujanivijay ♦ 4.5k • updated 23 months ago by Puli Chandramouli Reddy • 180
6
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1
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1.1k
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1
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How to download all sequences of a list of proteins for a particular organism
entrez direct efetch esearch written 24 months ago by traviata • 10 • updated 24 months ago by Kevin Blighe ♦ 50k
0
votes
1
answer
606
views
1
answer
Nested loops write in xml
python loop biopython efetch xml written 2.1 years ago by Lilizine • 0
1
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1
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1.1k
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1
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NCBI Entrez - efetch from PMC returns only abstract
efetch entrez pmc written 2.2 years ago by chaniart • 0 • updated 2.2 years ago by Jean-Karim Heriche ♦ 21k
10
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1
answer
2.9k
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11 follow
1
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Download NCBI genomes using taxonomy id (taxid)
ncbi python efetch biopython written 2.6 years ago by David • 160 • updated 2.2 years ago by pedrorodrigues • 10
1
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0
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1.2k
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0
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Entrez progammaticly: Direct efetch or epost + efetch
epost efetch entrez written 2.2 years ago by guedes.aureliano • 0
0
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1
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1.1k
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1
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URL for NCBI Efetch + XML with full annotation table
ncbi xml efetch eutils annotation written 2.3 years ago by Pierre Lindenbaum ♦ 123k • updated 2.3 years ago by genomax ♦ 73k
2
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1
answer
789
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1
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Mistakes in a bash script for adding taxid for nt database
taxid efetch nt database shell bash written 2.3 years ago by wyc661217 • 10 • updated 2.3 years ago by Istvan Albert ♦♦ 81k
0
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1
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1.1k
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1
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Transfer GI to taxID by efetch in a loop
software error taxid efetch gi written 2.4 years ago by wyc661217 • 10
0
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1
answer
1.3k
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1
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Using efetch(biopython) to get the fasta file of an mRNA, as well as the exon locations
python efetch biopython entrez written 2.4 years ago by Jacob • 10 • updated 2.4 years ago by Ben • 50
7
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1
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761
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1
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Extract Bibliographic Reference from GEO dataset using EFetch?
geo ncbi efetch written 2.5 years ago by Tom • 20 • updated 2.5 years ago by Santosh Anand ♦ 5.0k
3
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2
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3.5k
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2
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Difference between NCBI Entrez formats (e.g., xml, docsum) for efetch
ncbi edirect efetch entrez command-line written 5.5 years ago by paulparsons • 130 • updated 2.5 years ago by DCGenomics • 320
0
votes
0
answers
891
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0
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Getting DNA sequences by ncbi eutils for a specific assembly e.g.: hg19, hg38, GRCh37.p13 or GRCh38.p6?
ncbi eutils efetch dna sequences written 2.8 years ago by burcakotlu • 40
4
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2
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1.9k
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2
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How can we download all TSA and WGS from NCBI Trace by taxon programmatically?
ncbi assembly trace efetch eutils written 3.0 years ago by Michael Dondrup ♦ 46k
0
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2
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1.8k
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2
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How to retrieve any and all NCBI/GenBank accession numbers from a Taxonomy ID?
ncbi accession number efetch taxid bioinformatics written 3.0 years ago by yarmda • 0
0
votes
1
answer
825
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1
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How to pass multiple seq_start and seq_stop statements to NCBI efetch
ncbi efetch sequence entrez written 3.1 years ago by massa.kassa.sc3na • 90
1
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1
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2.5k
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1
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How to get correct Taxonomy UID from NCBI Taxonomy using Entrez E-utilities efetch?
ncbi efetch entrez biopython e-utilities written 3.3 years ago by JV • 380 • updated 3.3 years ago by piet • 1.7k
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