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102,957 results • Page
1 of 2060
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1
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Which atoms are not found in protein PDB files?
pdb
protein
just now by
user366312
▴ 10
0
votes
1
reply
22
views
Feedback on Workflow
WGS
pipeline
updated 14 minutes ago by
Asaf
8.9k • written 56 minutes ago by
01de
▴ 10
0
votes
0
replies
6
views
Which one is the smallest but the most complex PDB file?
pdb
protein
25 minutes ago by
user366312
▴ 10
0
votes
0
replies
9
views
Indel size seemingly capped by software?
indels
nucmer
33 minutes ago by
mrmrwinter
▴ 30
1
vote
3
replies
42
views
Downloading a huge amount of Fastq files
fastq
download
57 minutes ago by
davidmaimoun
• 0
1
vote
2
replies
28
views
DESEQ2 study design for different time points between controls and high dose samples.
drug
DEGs
DESEQ2
exposure
22 minutes ago by
salman_96
▴ 50
0
votes
1
reply
18
views
Metagenomic Binning: before or after denovo assembly?
denovo
metagenomic
assembly
binning
updated 21 minutes ago by
Asaf
8.9k • written 1 hour ago by
gatheringdusthere
▴ 20
0
votes
1
reply
24
views
high frequency subsequences
FASTA
tools
biopython
updated 50 minutes ago by
lieven.sterck
14k • written 2 hours ago by
setschmann
▴ 10
0
votes
0
replies
15
views
Rankprod
gene
differential
expression
analysis
Rankprod
2 hours ago by
nishimalhotra2612
▴ 20
0
votes
4
replies
135
views
UniProt REST Mapping Problem
UniProt
mapping
Python
REST
Ensembl
updated 2 hours ago by
a.zielezinski
10k • written 12 hours ago by
ngarber
• 0
0
votes
0
replies
22
views
Obtain FREQ column for a summary statistics
Statistic
Summary
Freq
MAF
3 hours ago by
Mahan
▴ 70
0
votes
1
reply
683
views
qp3pop missing pop error?
q3Pop
Admixtools
f3test
updated 3 hours ago by
francesco.fontani2
• 0 • written 23 months ago by
sam980406
• 0
0
votes
1
reply
102
views
Understanding ABI Sanger File Format
Sequencing
Sanger
Python
ABI
updated 3 hours ago by
trausch
★ 1.8k • written 6 days ago by
oludhe
▴ 30
0
votes
1
reply
37
views
bedgraphToBigWig error
Bedgraph
ucscPath
BigWig
R
updated 1 hour ago by
GenoMax
117k • written 3 hours ago by
Mireia
• 0
0
votes
0
replies
23
views
How can I understand aggregate in FAN-C tool using Hi-C data?
Hi-C
TAD
FAN-C
aggregate
fanc
3 hours ago by
woongjaej
▴ 20
0
votes
0
replies
26
views
interpretation of CNVKIT plot
deletion
homozygous
how
interpret
to
3 hours ago by
chenglei1865
• 0
8
votes
6
replies
2.1k
views
6 follow
Assembler for only nanopore data
genomics
Assembly
ONT
Abyss
updated 4 hours ago by
colindaven
★ 3.9k • written 3.2 years ago by
ringourquia
▴ 20
678
votes
160
replies
89k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 10 weeks ago by
Biostar
860 • written 5.6 years ago by
Istvan Albert
93k
6
votes
3
replies
146
views
Bulk RNA-seq with genome but without gene annotation
GFT
wouthou
analysisz
RNA-seq
updated 4 hours ago by
colindaven
★ 3.9k • written 1 day ago by
Diego
▴ 10
1
vote
0
replies
31
views
News:
Data analysis with the Tidyverse in July (18th-21st).
manipulation
Tidyverse
Data
Visualization
R
analysis
4 hours ago by
carlopecoraro2
★ 2.1k
0
votes
8
replies
89
views
could not find function "pickSoftThreshold"
ERROR
updated 1 hour ago by
andres.firrincieli
★ 2.5k • written 5 hours ago by
Sonia
• 0
0
votes
2
replies
60
views
Pearson correlation matrix heat map. The different colors represent Pearson correlation coefficients, and the diverse circle sizes represent P value.
bubble
R
plot
correlation
updated 5 hours ago by
Asaf
8.9k • written 5 hours ago by
Fahmida Khanam
• 0
0
votes
1
reply
65
views
Multiple copies of same gene annotated
CDS
Gene
Prokka
updated 8 hours ago by
Mensur Dlakic
★ 19k • written 8 hours ago by
SK007
• 0
1
vote
1
reply
94
views
how can i fix this problem in R
DESeq2
S4Vectors
updated 6 hours ago by
cpad0112
21k • written 10 hours ago by
Habib
• 0
0
votes
0
replies
68
views
Output dosage file by PLINK or other software
pgen
bed
plink
dosage
output
11 hours ago by
Roxy
• 0
1
vote
2
replies
103
views
bowtie2 error "Unable to read file magic number"
fastq
Bowtie2
updated 3 hours ago by
ATpoint
62k • written 13 hours ago by
rottenwasabi
• 0
0
votes
1
reply
94
views
david ID conversion
tag
conversion
locus
ID
david
updated 13 hours ago by
GenoMax
117k • written 14 hours ago by
hana
• 0
0
votes
0
replies
57
views
Bio.motifs.threshold module
PSSM
Bio.motif
13 hours ago by
nicoyanovsky
• 0
1
vote
1
reply
76
views
What is an acceptable pairwise alignment % for a MSA
MSA
MUSCLE
updated 14 hours ago by
Mensur Dlakic
★ 19k • written 16 hours ago by
aframirez
• 0
0
votes
0
replies
44
views
WGS based variant analysis for biomarkers
WGS
sequencing
statistics
14 hours ago by
halo22
▴ 280
0
votes
2
replies
143
views
Use of Scater for QC in scRNA-seq Analysis: How to remove cells with less than certain number of genes supported with certain number of reads
SingleCellExperiment
9 hours ago by
otieno43
• 0
0
votes
1
reply
91
views
Find motif position given a set of enrich peaks
peaks
position
Motif
updated 16 hours ago by
tobiaminuxy
• 0 • written 1 day ago by
Abdelhamid
• 0
0
votes
0
replies
53
views
No module named 'msprime'
module
python
msprime
no
vscode
17 hours ago by
desptsp
• 0
1
vote
3
replies
132
views
Retrieve protein sequence from Mgnify given only accession code
Mgnify
API
updated 14 hours ago by
GenoMax
117k • written 17 hours ago by
jscience
• 0
0
votes
1
reply
74
views
Intergenic distance
gene
gff
bioinformatics
updated 17 hours ago by
Trivas
▴ 390 • written 17 hours ago by
h_asma
• 0
0
votes
0
replies
47
views
Find motifs close to nanog motifs from Fimo output
fimo
18 hours ago by
tobiaminuxy
• 0
1
vote
1
reply
101
views
What are the data values in qRT-PCR for statistical testing? dCT? or 2^-dCT?
qRT-PCR
updated 18 hours ago by
karl.stamm
4.0k • written 19 hours ago by
YCW121
• 0
0
votes
1
reply
79
views
How can I transform a three column data frame into a binary-table in R?
rstudio
updated 17 hours ago by
brunobsouzaa
▴ 720 • written 18 hours ago by
Camilo Andres
• 0
0
votes
4
replies
152
views
[R] Differential Co-Expression ?
R
edgeR
GEO
2 hours ago by
ali
▴ 20
2
votes
2
replies
239
views
It is weird there are no reads less than 100 bp in qualimap.
qualimap
16 hours ago by
lidan0001
▴ 30
0
votes
0
replies
55
views
What is the differences between using Shared Sequence Variants and OTUs?
genomics
18 hours ago by
Phú
• 0
0
votes
0
replies
51
views
Getting gene names in ballgown object
gtf
ballgown
analysis
19 hours ago by
Katherine
• 0
0
votes
0
replies
53
views
Differential expression with single cell data: any good two component (hurdle) models after MAST?
next-gen
cell
single
RNA-Seq
sequencing
MAST
19 hours ago by
ntuzov
• 0
0
votes
0
replies
57
views
Getting pocket sequence information by using Fpocket
binding
fpocket
pocket
protein
17 hours ago by
drbioengineer
• 0
0
votes
1
reply
133
views
Job:
Need a RNASeq Analysis tutor
rnaseq
tutor
analysis
differential
updated 18 hours ago by
Mensur Dlakic
★ 19k • written 20 hours ago by
smithkthedale
• 0
0
votes
0
replies
57
views
[R] Extract Normalized Counts from DGEList (edgeR) ?
R
edgeR
GEO
20 hours ago by
ali
▴ 20
0
votes
1
reply
127
views
Job:
Opportunity at GRAIL | Staff Bioinformatics Scientist - Post Diagnostic Applications
hiring
updated 20 hours ago by
cpad0112
21k • written 20 hours ago by
Shawn Vyas
• 0
0
votes
0
replies
50
views
MERLIN haplotyping
MERLIN
20 hours ago by
smb2174
• 0
0
votes
0
replies
52
views
STR expansion detection on IonTorrent WES data?
repeat
STR
IonTorrent
wes
ngs
short
tandem
20 hours ago by
Joel Wallenius
▴ 90
0
votes
0
replies
47
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
20 hours ago by
bnayer26
• 0
102,957 results • Page
1 of 2060
Recent Votes
A: PLINK logistic regression analysis and covariates
C: PLINK logistic regression analysis and covariates
PLINK logistic regression analysis and covariates
A: Annotating/Finding "NNNNNN" scaffold gaps in genome assembly
Comment: DESEQ2 study design for different time points between controls and high dose sam
A: BWA mem bam output name sorted
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Popular Question
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sg197
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Recent Replies
Answer: Feedback on Workflow
by
Asaf
8.9k
There are already pipelines in place for everything these days. If this is your first time working with NGS and the sequencing is pretty st…
Comment: Metagenomic Binning: before or after denovo assembly?
by
Asaf
8.9k
binning based on what? Kraken assignment or something like that? What about the unmapped reads or reads mapped at higher taxonomic levels?
Comment: DESEQ2 study design for different time points between controls and high dose sam
by
salman_96
▴ 50
Hi, Thank you for responding. The column Groups of interests contains information about both (other columns) condition and time_days. Woul…
Comment: high frequency subsequences
by
lieven.sterck
14k
you might want to have a look at Kmer counting tools such as JellyFish, KAT, ntCard and such
Comment: Downloading a huge amount of Fastq files
by
davidmaimoun
• 0
Yes sorry, By huge I meant about **400K** genomes of salmonella. And by years, I really don't know. For instance, I wanted to try COBS…
Comment: DESEQ2 study design for different time points between controls and high dose sam
by
ATpoint
62k
Yes, that so-called "full factorial" design would be the easiest while catching all the experimental factors. Check `contrasts` in the vig…
Comment: could not find function "pickSoftThreshold"
by
andres.firrincieli
★ 2.5k
Install [impute][1] and you should be fine [1]: https://www.bioconductor.org/packages/release/bioc/html/impute.html
Comment: Downloading a huge amount of Fastq files
by
Arup Ghosh
2.9k
Try the [ASPERA client][1] CLI. [1]: https://www.ncbi.nlm.nih.gov/public/
Comment: Which miRNA arm to select for target prediction, 3p or 5p?
by
Tusharika
• 0
Thanks! I have used the miRNA dataset from XenaBrowser and ran the Differential Expression pipeline on it using the DESeq2 Bioconductor pac…
Comment: Downloading a huge amount of Fastq files
by
ATpoint
62k
Would you mind adding some details. What do you download, what is "huge", why do you think it takes "years", what are your commands and wha…
Comment: Bacterial contamination in human DNA sample
by
Arup Ghosh
2.9k
Try taxonomical classification of the reads using [Kraken2][1] or similar tools. [1]: https://ccb.jhu.edu/software/kraken2/
Comment: bedgraphToBigWig error
by
Arup Ghosh
2.9k
Make sure you have [UCSCtools][1] available in the mentioned location. If you are using [E-myers/rnaseq][2] , the bedgraphToBigWig functio…
Comment: could not find function "pickSoftThreshold"
by
Sonia
• 0
Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there…
Comment: How to find DEG within a cluster between two groups without any replication info
by
piyushjo
▴ 650
Ok. I don't think you need to care about replicates here. If you are just merging the data and your replicates form separate cluster, then…
Answer: UniProt REST Mapping Problem
by
a.zielezinski
10k
Here is an example how to access UniProt's REST with Python 3 with the `requests` package (`pip install requests`). import json …
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