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Showing :
questions
0
votes
4
replies
1.7k
views
Appending sequences to downloaded NCBI nt database
ncbi
blastdb_alias
makeblastdb
3.4 years ago by
Biogeek
▴ 470
1
vote
3
replies
702
views
Retrieve multiple refseq genomes in seperate fasta files
ncbi
Refseq
updated 13 months ago by
Ram
43k • written 3.8 years ago by
Biogeek
▴ 470
0
votes
0
replies
1.6k
views
Bioinformatics workstation Spec advice: Metagenomics
workstation
RAM
metagenomics
4.0 years ago by
Biogeek
▴ 470
0
votes
0
replies
1.2k
views
Confused with Fishers test for GO enrichment
fishers
Enrichment
input
5.0 years ago by
Biogeek
▴ 470
2
votes
4
replies
2.0k
views
Example of gene2cat goseq
goseq
updated 5.0 years ago by
cfos4698
★ 1.1k • written 5.0 years ago by
Biogeek
▴ 470
7
votes
11
replies
1.9k
views
Split comma seperated list of GO terms into multiple rows and maintain gene identifier in each
Gene ontology
data manipulation
updated 5.0 years ago by
st.ph.n
★ 2.7k • written 5.0 years ago by
Biogeek
▴ 470
4
votes
2
replies
5.6k
views
ReviGO down, any alternatives for GO enrichment condensing?
revigo
GO enrichment
topgo
simrel
updated 5.0 years ago by
Berghopper
▴ 20 • written 5.0 years ago by
Biogeek
▴ 470
0
votes
0
replies
835
views
Enrichment via simple Fishers exact: Combine or not?
go
enrichment
fishers
statistics
5.0 years ago by
Biogeek
▴ 470
1
vote
2
replies
1.1k
views
slurm Exceeded step memory limit: Interleaving FastQ files
fastq
slurm
5.1 years ago by
Biogeek
▴ 470
1
vote
4
replies
1.9k
views
Sequencing (+1bp in length?) and adaptor trimming.
RNA-Seq
sequencing
adapters
updated 5.1 years ago by
GenoMax
141k • written 5.1 years ago by
Biogeek
▴ 470
0
votes
2
replies
1.7k
views
weird e-values with rapsearch
rapsearch
e-values
updated 5.2 years ago by
ATpoint
81k • written 7.5 years ago by
Biogeek
▴ 470
4
votes
7
replies
3.7k
views
7 follow
Get -400bp to +50bp sequence of gene from gff3 file
upstream
downstream
promoter
motifs
updated 21 months ago by
Shannon
• 0 • written 5.2 years ago by
Biogeek
▴ 470
1
vote
1
reply
2.0k
views
Gene correlation analysis after deseq2
deseq2
correlation
clustering
updated 5.3 years ago by
dqz377977905
• 0 • written 5.3 years ago by
Biogeek
▴ 470
2
votes
2
replies
1.9k
views
Multiple fasta file : calculate % composition of amino acids
amino acids
composition
calculate
updated 5.3 years ago by
Pierre Lindenbaum
161k • written 5.3 years ago by
Biogeek
▴ 470
0
votes
3
replies
1.3k
views
Refseq accessions - getting gene function and GO terms for each one
refseq
gene function
gene ontology
5.4 years ago by
Biogeek
▴ 470
0
votes
1
reply
1.1k
views
Refseq vs original genome assembly and issues
refseq
genome alignment
annotation
5.4 years ago by
Biogeek
▴ 470
3
votes
3
replies
5.6k
views
STAR two -pass mode - lower alignment rate than one pass mode?
star
alignment
two pass mode
updated 2.4 years ago by
FantasticAI
▴ 60 • written 5.4 years ago by
Biogeek
▴ 470
4
votes
8
replies
1.3k
views
NCBI genome version vs published genome version - what's 'better'?
genome
resources
ncbi genome
published genome
5.4 years ago by
Biogeek
▴ 470
4
votes
4
replies
1.1k
views
mRNA / Protein Annotation questions - etiquette and consensus
Genome
Out-dated
Re-annotation
blastx
blastp
updated 5.4 years ago by
lieven.sterck
15k • written 5.4 years ago by
Biogeek
▴ 470
1
vote
7
replies
1.5k
views
Genome-aligned RNA-Seq: one treatment showing high% of unmapped reads:too short
RNA-Seq
mapping
low alignment
GC content
5.5 years ago by
Biogeek
▴ 470
0
votes
3
replies
3.0k
views
Going from BlastX to GO annotation
Annotation
blastx
GO
ONTOLOGY
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
Biogeek
▴ 470
1
vote
3
replies
3.7k
views
Biological variation within replicate groups, not much DE
biological variation
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
Biogeek
▴ 470
1
vote
0
replies
1.8k
views
Pathway enrichment and interaction analysis of genes in plants?
interaction
pathway enrichment
updated 5.6 years ago by
Biostar
20 • written 7.6 years ago by
Biogeek
▴ 470
0
votes
0
replies
1.2k
views
Conditional reciprocal blast confusion
crb-blast
6.1 years ago by
Biogeek
▴ 470
6
votes
2
replies
1.4k
views
QTL /linkage trait mapping
QTL / linkage trait mapping
updated 6.2 years ago by
andrew.j.skelton73
6.5k • written 6.2 years ago by
Biogeek
▴ 470
5
votes
13
replies
10k
views
Heatmap.2 - flip dendrogram so control group appears on LHS?
R
heatmap
updated 6.5 years ago by
e.rempel
★ 1.1k • written 6.5 years ago by
Biogeek
▴ 470
4
votes
4
replies
5.1k
views
choosing a suitable max intron size for STAR (plant alignment)
intron size
star
plants
updated 6.7 years ago by
claudiorivero92
• 0 • written 7.7 years ago by
Biogeek
▴ 470
3
votes
3
replies
5.5k
views
Can you pool individuals to make 1 biological replicate?
biological-replicates
RNA-Seq
updated 15 months ago by
Ram
43k • written 8.9 years ago by
Biogeek
▴ 470
0
votes
1
reply
1.5k
views
Easier way to filter contaminants based on protein similarity ?
diamond
blastx
uniprot
trembl
updated 7.5 years ago by
Elisabeth Gasteiger
★ 2.4k • written 7.5 years ago by
Biogeek
▴ 470
0
votes
0
replies
1.3k
views
Do I need to re-normalize?
RNA-Seq
normalization
7.5 years ago by
Biogeek
▴ 470
1
vote
9
replies
4.2k
views
Parsing uniprot .dat files
Annotation
uniprot
parsing
updated 7.6 years ago by
Elisabeth Gasteiger
★ 2.4k • written 7.7 years ago by
Biogeek
▴ 470
9
votes
4
replies
3.7k
views
STAR BAM into RSEM
RSEM
star
forward-prob
updated 7.6 years ago by
Devon Ryan
104k • written 7.6 years ago by
Biogeek
▴ 470
1
vote
4
replies
2.5k
views
HIGH BCV in EdgeR, any ideas?
EdgeR
BCV
GLM
high dispersion
7.6 years ago by
Biogeek
▴ 470
1
vote
5
replies
4.0k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 10 months ago by
Ram
43k • written 7.6 years ago by
Biogeek
▴ 470
0
votes
2
replies
1.7k
views
Experience with SOAP trans
soap trans
de novo
updated 7.6 years ago by
Biostar
20 • written 7.7 years ago by
Biogeek
▴ 470
3
votes
7
replies
2.7k
views
tr2aacds memory issues
tr2aacds
evidential gene
memory issues
updated 7.7 years ago by
gilbert.bionet
▴ 160 • written 7.7 years ago by
Biogeek
▴ 470
0
votes
1
reply
2.1k
views
SOAPdenovo trans min contig issue
soapdenovo
updated 13 months ago by
Ram
43k • written 7.7 years ago by
Biogeek
▴ 470
5
votes
10
replies
2.2k
views
BBmerge and gaining insert size / SOAP question
bbmerge
bbtools
soaptrans
de novo
7.7 years ago by
Biogeek
▴ 470
3
votes
3
replies
5.9k
views
Annoying STAR aligner problem
STAR
aligner
7.7 years ago by
Biogeek
▴ 470
3
votes
6
replies
2.9k
views
Merging all left / all right reads before STAR align?
RNA-Seq
genome
7.7 years ago by
Biogeek
▴ 470
3
votes
2
replies
2.3k
views
Thoughts on a few bad tiles per sequencing run
tiles
sequencing
updated 7.7 years ago by
Devon Ryan
104k • written 7.7 years ago by
Biogeek
▴ 470
3
votes
8
replies
3.6k
views
Alignment of seq reads to a genome, process after STAR?
genome
rnaseq
reference genome
updated 7.7 years ago by
Devon Ryan
104k • written 7.7 years ago by
Biogeek
▴ 470
3
votes
3
replies
1.5k
views
Should I be using the reference genome
Genome
rnaseq
updated 7.7 years ago by
Brian Bushnell
20k • written 7.7 years ago by
Biogeek
▴ 470
0
votes
4
replies
1.6k
views
blast x results - some making no sense
blastx
updated 7.8 years ago by
Chris Fields
★ 2.2k • written 7.8 years ago by
Biogeek
▴ 470
1
vote
0
replies
1.9k
views
High in group variability RNA seq
rna-seq
updated 7 months ago by
Ram
43k • written 7.8 years ago by
Biogeek
▴ 470
0
votes
3
replies
1.9k
views
Any tools out there for Interproscan enrichment analysis?
IPS
enrichment
hypergeometric
updated 7.9 years ago by
Jean-Karim Heriche
27k • written 7.9 years ago by
Biogeek
▴ 470
0
votes
1
reply
1.5k
views
Help re-formatting an Interproscan file
interproscan
Reformat
updated 13 months ago by
Ram
43k • written 7.9 years ago by
Biogeek
▴ 470
1
vote
11
replies
2.1k
views
RNA-Seq of environmental samples
environmental samples
RNA-Seq
contamination
8.0 years ago by
Biogeek
▴ 470
0
votes
2
replies
1.7k
views
Simple question: obtaining GO terminology utilizing NCBI GI's
ncbi
annotation
GO
8.0 years ago by
Biogeek
▴ 470
0
votes
2
replies
4.0k
views
EdgeR filter thresholds
edger
DIFFERENTIAL EXPRESSION
updated 8.0 years ago by
GouthamAtla
12k • written 8.0 years ago by
Biogeek
▴ 470
68 results • Page
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