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13,534 results • Page
1 of 271
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Replies
0
votes
1
reply
484
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 39 minutes ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
0
replies
15
views
Odd alignment question/finding
Alignment
44 minutes ago by
poordumbsillyidiot
• 0
0
votes
1
reply
67
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 1 hour ago by
GenoMax
141k • written 5 hours ago by
mgranada3
▴ 30
0
votes
0
replies
35
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
6 hours ago by
meck
• 0
0
votes
0
replies
52
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 4 hours ago by
Ram
43k • written 6 hours ago by
Oscar
▴ 10
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
6
replies
363
views
Post-imputation plot
michigan-imputation-server
quality-control
4 hours ago by
kl
▴ 10
0
votes
1
reply
143
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 8 hours ago by
Adam
▴ 30 • written 1 day ago by
J
• 0
1
vote
3
replies
212
views
DESeq2 processing problems
deseq2
R
updated 8 hours ago by
ATpoint
82k • written 18 hours ago by
jagdish7921
• 0
1
vote
4
replies
141
views
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
6 hours ago by
nicole.kavanagh
• 0
0
votes
1
reply
716
views
cnetplot category names are too long
RNASeq
clusterprofiler
cnetplot
enrichplot
updated 10 hours ago by
bkleiboeker
▴ 370 • written 2.7 years ago by
carov
• 0
0
votes
1
reply
80
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 8 hours ago by
Ram
43k • written 10 hours ago by
ernestine.kubi
• 0
0
votes
0
replies
51
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
10 hours ago by
VITALA
• 0
0
votes
1
reply
145
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 22 hours ago by
Ram
43k • written 1 day ago by
rianna.collins
• 0
0
votes
1
reply
125
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 16 hours ago by
i.sudbery
19k • written 1 day ago by
Edmond
• 0
0
votes
0
replies
93
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
1 day ago by
O.rka
▴ 710
0
votes
1
reply
290
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 22 hours ago by
Ram
43k • written 1 day ago by
Dr Huma Naz
• 0
2
votes
2
replies
213
views
p-value in CIBERSORT
CIBERSORT
p-value
17 hours ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
292
views
Telescope issue
Telescope
RNA-seq
updated 10 hours ago by
GenoMax
141k • written 1 day ago by
eleven11
• 0
5
votes
6
replies
439
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 day ago by
me
▴ 760 • written 2 days ago by
Mariana
▴ 40
1
vote
1
reply
182
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 1 day ago by
Ram
43k • written 1 day ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
242
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
14 hours ago by
Nafi
• 0
1
vote
3
replies
227
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 1 day ago by
GenoMax
141k • written 1 day ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
182
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Dora
▴ 10
0
votes
0
replies
128
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 1 day ago by
Ram
43k • written 1 day ago by
Chakri
• 0
0
votes
1
reply
141
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 8 hours ago by
Adam
▴ 30 • written 1 day ago by
Ahiad Chen Zion
• 0
0
votes
4
replies
226
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 1 day ago by
Michael
54k • written 1 day ago by
Riccardo
▴ 10
0
votes
0
replies
100
views
barcode of TCR-sequencing
barcode
1 day ago by
yueli7
▴ 250
0
votes
0
replies
103
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
99
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 1 day ago by
Ram
43k • written 1 day ago by
Alexandros
• 0
0
votes
1
reply
135
views
unable to get feature count results
featureCounts
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
0
replies
99
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
0
votes
3
replies
240
views
KEGG Pathways
r
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Sudip
• 0
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 1 day ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
103
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
1 day ago by
Bine
▴ 60
0
votes
1
reply
253
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
1 day ago by
David Langenberger
11k
0
votes
0
replies
108
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
1 day ago by
8armed
• 0
0
votes
1
reply
158
views
Deseq2
Deseq2
updated 1 day ago by
Jack Tierney
▴ 360 • written 1 day ago by
Sudip
• 0
1
vote
1
reply
193
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 1 day ago by
Michael
54k • written 2 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
233
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 1 day ago by
Lluís R.
★ 1.2k • written 1 day ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
168
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Sudip
• 0
1
vote
2
replies
196
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
0
replies
95
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
0
replies
98
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
1 day ago by
fanglujing
▴ 60
0
votes
0
replies
115
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
3
replies
720
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
235
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 1 day ago by
Ram
43k • written 2 days ago by
Hamtaro
▴ 50
0
votes
1
reply
164
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
0
votes
3
replies
260
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 day ago by
GenoMax
141k • written 2 days ago by
kim
• 0
3
votes
2
replies
349
views
Extract protein sequence
fasta
alignment
blast
1 day ago by
anna
▴ 20
13,534 results • Page
1 of 271
Recent Votes
Comment: Can't install AnnotationHub
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
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Recent Replies
Answer: Basic stats in hierfstat
by
mdav
• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p
by
GenoMax
141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long
by
bkleiboeker
▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue
by
GenoMax
141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery
by
GenoMax
141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
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