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8
votes
4
replies
1.6k
views
Plot genes along scaffolds and sort scaffolds according to their length
R plot genes scaffold
updated 3 months ago by ▴ 90 • written 3.7 years ago by ▴ 130
2
votes
1
reply
401
views
How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank?
genbank
11 months ago by Chvatil ▴ 130
2
votes
1
reply
673
views
Looking for Synteny blocks database in arthopods
database synteny
updated 2.4 years ago by ★ 3.8k • written 2.4 years ago by ▴ 130
4
votes
7
replies
2.0k
views
Download all Becteria and protist fasta protein sequences from UNIPROT proteomes
uniprot fetch fasta proteome bash
2.8 years ago by Chvatil ▴ 130
0
votes
0
replies
429
views
Gene ontology analysis on viral proteins
gene go ontology
2.9 years ago by Chvatil ▴ 130
2
votes
11
replies
1.9k
views
Using snakemake in order to download reads and run hisat2 mapping
hisat2 snakemake python
updated 3.0 years ago by 22k • written 3.0 years ago by ▴ 130
0
votes
1
reply
844
views
Add features on newick tree (then by creating a NHX format)
newick nhx phylogeny python r
3.2 years ago by Chvatil ▴ 130
7
votes
1
reply
1.2k
views
Calculate tetranucleotide frequency deviation on python
biopython python TNFs
updated 3.3 years ago by ★ 27k • written 3.3 years ago by ▴ 130
0
votes
1
reply
619
views
Find repeat regions on 100 eukaryotic assemblies
repeat Assembly
updated 3.4 years ago by 6.4k • written 3.4 years ago by ▴ 130
0
votes
4
replies
1.3k
views
Question about codeml
codeml paml phylogeny tree ds
updated 2.5 years ago by ▴ 190 • written 3.4 years ago by ▴ 130
0
votes
0
replies
1.1k
views
Runmode = -2 in Biopython PAML impossible ?
paml codeml biopython python3
3.4 years ago by Chvatil ▴ 130
0
votes
0
replies
695
views
Programme to calculate dN/dS between pair of sequences in a seq alignment
gene dn/ds codeml paml sequence
3.5 years ago by Chvatil ▴ 130
3
votes
1
reply
763
views
Extract specific variant genome ID from a VCF file
variant genome vcf
updated 3.5 years ago by 14k • written 3.5 years ago by ▴ 130
3
votes
5
replies
2.1k
views
Difference between mate-pair, paired-end and long read
assembly read
3.5 years ago by Chvatil ▴ 130
0
votes
0
replies
544
views
retrieve the properties of the reads on NCBI on the command line
Assembly reads ncbi
3.5 years ago by Chvatil ▴ 130
0
votes
0
replies
544
views
detect and correct misassemblies in eucaryotic scaffolds
reapr mec Assembly
3.6 years ago by Chvatil ▴ 130
2
votes
5
replies
5.2k
views
HISAT2- (ERR): hisat2-align exited with value 134
hisat mapping
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by ▴ 130
2
votes
3
replies
5.1k
views
Size of the nr database fasta file?
nr ncbi database
updated 3.8 years ago by ▴ 460 • written 3.8 years ago by ▴ 130
3
votes
2
replies
817
views
Eucaryotic gene predictor within eucaryote genome
gene
updated 3.8 years ago by 8.6k • written 3.8 years ago by ▴ 130
0
votes
0
replies
1.1k
views
disable the SRA cache in HISAT2
hisat rnaseq mapping
3.8 years ago by Chvatil ▴ 130
0
votes
3
replies
769
views
Test if a list of genes with coordinates are expressed (hisat2 data)
RNA-Seq transcription
updated 3.9 years ago by ▴ 230 • written 3.9 years ago by ▴ 130
0
votes
6
replies
1.6k
views
Using Bowtie and SRA mode
bowtie mapping
3.9 years ago by Chvatil ▴ 130
0
votes
2
replies
1.4k
views
Create my own universel GO db from QuickGO in R
GO ontology R
4.0 years ago by Chvatil ▴ 130
0
votes
1
reply
751
views
Plot loci on scaffold (graphic visualization in command line)
sequence genome scaffold
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 130
0
votes
1
reply
667
views
Find informations about virus families and their genomic structure
ncbi
4.1 years ago by Chvatil ▴ 130
1
vote
4
replies
839
views
Get sequencing informations from NCBI with acc number
ncbi Assembly efetch
4.1 years ago by Chvatil ▴ 130
1
vote
3
replies
2.5k
views
Get distance matrix based on node tree
tree distance matrix phylogeny
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 130
0
votes
0
replies
697
views
Codon substitution model (codeml)
dnds codeml paml
updated 4.2 years ago by 20 • written 4.4 years ago by ▴ 130
1
vote
4
replies
1.3k
views
Remove sequence by coordinates with Biopython
biopython fasta
4.3 years ago by Chvatil ▴ 130
0
votes
1
reply
996
views
Hisat2 --sra-acc option (redirect sra file to a desired directory)
hisat2 sra ncbi
4.4 years ago by Chvatil ▴ 130
3
votes
5
replies
1.3k
views
Set the max coverage wanted with Hisat2 ?
Hisat2 mapping
4.4 years ago by Chvatil ▴ 130
3
votes
10
replies
1.7k
views
Access to SRA read from a specific genome assembly on NCBI
ncbi Assembly reads
4.4 years ago by Chvatil ▴ 130
1
vote
4
replies
1.2k
views
Use esearch on python to get nucleotide sequence from the protein ses id
esearch python entrez
4.5 years ago by Chvatil ▴ 130
0
votes
0
replies
944
views
Get pvalue and/or confidence interval of dN/dS from the codeml output
python dNdS
4.5 years ago by Chvatil ▴ 130
0
votes
2
replies
702
views
Recover from protein ID the corresponding nucleotide ID .
fasta python ncbi
updated 4.5 years ago by ▴ 600 • written 4.5 years ago by ▴ 130
4
votes
2
replies
1.5k
views
Count number of monophyletic groups within pylogeny
phylogeny monophyletic
updated 5.0 years ago by 21k • written 5.0 years ago by ▴ 130
0
votes
0
replies
901
views
What kind of protein matrix substitution use for blastX divergent sequences
blast diamond homology matrix
5.2 years ago by Chvatil ▴ 130
6
votes
23
replies
6.8k
views
Recover fasta sequences in database from the blast output 6
blast output fasta
5.3 years ago by Chvatil ▴ 130
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly assembler
updated 5.7 years ago by 20 • written 5.9 years ago by ▴ 130
0
votes
10
replies
2.9k
views
No output nr file after running makedb
blast diamond makedb
updated 5.8 years ago by 20 • written 6.0 years ago by ▴ 130
8
votes
22
replies
2.8k
views
6 follow
De novo assembly programm
assembly
5.8 years ago by Chvatil ▴ 130
6
votes
4
replies
4.8k
views
How to use ALLPATH-LG assembler
Assembly genome
updated 5.9 years ago by ▴ 140 • written 5.9 years ago by ▴ 130
7
votes
14
replies
9.2k
views
Parsing dataframe and sort a fasta file
python pandas fasta
updated 6.0 years ago by 5.3k • written 6.0 years ago by ▴ 130
3
votes
4
replies
7.4k
views
Counting number of reads and bases fastQ with python
fastq python biopython
updated 13 months ago by 43k • written 6.0 years ago by ▴ 130
0
votes
0
replies
867
views
Merge my dataframe depending on a fasta SeqId order
pandas python merge
6.0 years ago by Chvatil ▴ 130
2
votes
3
replies
2.4k
views
Get summary of augustus ouput (gff)
augustus gff
updated 6.0 years ago by ▴ 640 • written 6.0 years ago by ▴ 130
4
votes
13
replies
9.1k
views
Cannot install NumPy using pip and import it
numpy python
updated 6.0 years ago by ★ 2.1k • written 6.0 years ago by ▴ 130
0
votes
7
replies
1.3k
views
blastdbcmd issue
blast database db nr
updated 6.0 years ago by 142k • written 6.0 years ago by ▴ 130
0
votes
0
replies
1.1k
views
Filter reversed rows in a dataframe (pandas)
pandas python filtering
6.0 years ago by Chvatil ▴ 130
4
votes
6
replies
4.7k
views
change seq name in a fasta file with a dataframe
pandas python fasta
updated 6.0 years ago by ★ 2.0k • written 6.0 years ago by ▴ 130
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