Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
161 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
0
votes
2
replies
949
views
error while executing panX script (KeyError: 'db_xref').
linux
python
genome
biopython
updated 5 hours ago by
Ram
39k • written 2.8 years ago by
Kumar
▴ 100
1
vote
2
replies
183
views
hisat2 Error 137
hisat2
RNA-seq
2 days ago by
Forough
▴ 10
0
votes
2
replies
1.4k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer
Label-Free
Proteomics
updated 2 days ago by
Ram
39k • written 4.5 years ago by
k2bhide
▴ 80
0
votes
2
replies
1.7k
views
How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 12 hours ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
0
votes
2
replies
243
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
2 days ago by
demoraesdiogo2017
▴ 90
1
vote
2
replies
862
views
ATACseq libraries differ in each run
ChIP-Seq
sequencing
ATAC-seq
updated 6 hours ago by
Ram
39k • written 3.0 years ago by
rahel14350
▴ 40
3
votes
2
replies
881
views
Creating a genotype matrix for BeviMed
snp
genome
Bayesian
updated 7 hours ago by
Ram
39k • written 3.4 years ago by
tacrolimus
▴ 110
0
votes
2
replies
184
views
[python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must be integers)
TypeError
python
offtopic
updated 2 hours ago by
Ram
39k • written 7 weeks ago by
probioquestioner
• 0
1
vote
2
replies
231
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 5 days ago by
thadjudkins2
• 0 • written 5 days ago by
herh
• 0
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 1 day ago by
Ram
39k • written 6 days ago by
linnet.roque6
▴ 10
1
vote
2
replies
997
views
What is the minimum percentage of identity (blastp) to predict the orthologous genes in different species?
Assembly
gene
genome
alignment
updated 5 hours ago by
Ram
39k • written 2.7 years ago by
Kumar
▴ 100
1
vote
2
replies
209
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
6 days ago by
rheab1230
▴ 140
0
votes
2
replies
355
views
BedGraph to bigWig
bigWig
BedGraph
Galaxy
ATAC-seq
updated 6 hours ago by
Ram
39k • written 5 months ago by
abhay.kanodia
▴ 10
0
votes
2
replies
202
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
1 day ago by
mattze731
▴ 10
0
votes
2
replies
161
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
13 hours ago by
JACKY
▴ 100
0
votes
2
replies
1.0k
views
Find most upregulated genes in one library?
EdgeR
RNA-Seq
Rsubread
updated 2 days ago by
Ram
39k • written 3.7 years ago by
williams.damon26
▴ 10
0
votes
2
replies
302
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
1 day ago by
zhangdengwei
▴ 190
0
votes
2
replies
167
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
6 days ago by
survive
• 0
0
votes
2
replies
770
views
Error in mvnX when running processSamples.R of OncoCNV
variant-calling
oncocnv
cnv
updated 1 day ago by
Ram
39k • written 3.5 years ago by
mwarrier
• 0
1
vote
2
replies
522
views
How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
assembly
gene
genome
next-gen
updated 2 days ago by
Ram
39k • written 3.6 years ago by
Kumar
▴ 100
1
vote
2
replies
209
views
Combination of ROC CURVE
roccurve
R
AUC
3 days ago by
Maria17
▴ 20
1
vote
1
reply
602
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 5 days ago by
GenoMax
130k • written 5 days ago by
Mohd
▴ 20
0
votes
1
reply
866
views
deeptools plotHeatmap gives blurry pixelated image
computeMatrix
plotHeatmap
deeptools
ATAC-seq
updated 6 hours ago by
Ram
39k • written 2.4 years ago by
Himanshu C
• 0
0
votes
1
reply
714
views
MMSplice score interpretation
mmsplice
splice-effect-prediction
updated 5 hours ago by
Ram
39k • written 2.7 years ago by
Augusta
▴ 30
0
votes
1
reply
900
views
Strange output from Homer findPeaks
homer
atac-seq
updated 6 hours ago by
Ram
39k • written 3.5 years ago by
fr
▴ 200
0
votes
1
reply
934
views
ATAC seq enhancer help
alignment
ATAC-seq
bowtie2
DNA
Enhancers
updated 6 hours ago by
Ram
39k • written 3.7 years ago by
mrs.whirly
• 0
0
votes
1
reply
353
views
pal2nal -nogap -nomismatch options not working
pal2nal
updated 28 minutes ago by
Marie
• 0 • written 6 months ago by
pkfsantos
• 0
0
votes
1
reply
705
views
Is there bioinformatics tool to check cross hybridization between primers and probes?
primer
cross-hybridisation
pcr
updated 8 hours ago by
Tawny
▴ 180 • written 2.7 years ago by
Pramod Shinde
• 0
0
votes
1
reply
165
views
Merge different vcf files
vcf
updated 5 days ago by
Ram
39k • written 6 days ago by
caique.manochio
• 0
0
votes
1
reply
749
views
plasmid spades R1/R2 files?
plasmid
sequencing
updated 5 days ago by
Ram
39k • written 3.8 years ago by
sarah.goldstein
• 0
0
votes
1
reply
813
views
Filtering for homozygous reference alleles
SNP
sequence
genome
updated 5 days ago by
Ram
39k • written 3.7 years ago by
AGE
▴ 30
0
votes
1
reply
755
views
differential expression of geodataset using limma (input files)
R
gene
updated 7 hours ago by
Ram
39k • written 3.4 years ago by
firstorthopedicdoctor
▴ 30
2
votes
1
reply
1.8k
views
How do I apply a patch to hg38?
reference
human
freeze
hg38
patch
updated 6 days ago by
Jeremy Leipzig
21k • written 5.6 years ago by
imperialcommando117
• 0
0
votes
1
reply
823
views
Error in MEGAHIT
Assembly
next-gen
metagenomic
updated 8 hours ago by
Ram
39k • written 3.4 years ago by
nisrinalulu
▴ 10
1
vote
1
reply
83
views
switching from illumination to NEB prep kits
NEB
WGS
WES
illumina
updated 10 hours ago by
GenoMax
130k • written 11 hours ago by
lait
▴ 170
1
vote
1
reply
1.4k
views
How to analyze DNA data with UMI
next-gen-sequencing
umi
updated 2 hours ago by
Ram
39k • written 3.2 years ago by
deniselavezzari
• 0
0
votes
1
reply
874
views
Masters in Bioinformatics
masters
structural-bioinformatics
assistantship
updated 6 days ago by
Ram
39k • written 3.9 years ago by
Manvitha Reddy
▴ 10
0
votes
1
reply
147
views
Pairwise Alignment
Pairwise-Alignment
updated 2 days ago by
Ram
39k • written 3 days ago by
Fatemeh
• 0
0
votes
1
reply
261
views
Comparing loci across catalogs
Stacks
reference
alignment
RADseq
adegenet
updated 5 days ago by
rycro_c
• 0 • written 13 months ago by
Austin
• 0
0
votes
1
reply
162
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA
database
updated 3 days ago by
Hamid Ghaedi
2.9k • written 3 days ago by
younglin113
▴ 50
0
votes
1
reply
71
views
Visualizing several genomes/plasmids in a single figure
visualization
updated 9 hours ago by
GenoMax
130k • written 10 hours ago by
blur
▴ 270
0
votes
1
reply
80
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 10 hours ago by
ATpoint
72k • written 10 hours ago by
t.ru
▴ 20
0
votes
1
reply
70
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 10 hours ago by
ATpoint
72k • written 10 hours ago by
f2ff7a46
• 0
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read
plasmid
updated 6 days ago by
Ram
39k • written 3.9 years ago by
El Niño
▴ 10
0
votes
1
reply
85
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
updated 5 hours ago by
Ram
39k • written 9 hours ago by
aaronlogsdon2001
• 0
0
votes
1
reply
686
views
Small demo bioinformatics workflows which don't require reference data?
workflow
pipeline
updated 5 days ago by
Ram
39k • written 3.7 years ago by
steve
★ 3.3k
1
vote
1
reply
67
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated 8 hours ago by
GenoMax
130k • written 8 hours ago by
saint-even
• 0
0
votes
1
reply
36
views
How to add annotation columns with specific colors to the heatmap?
R
rnaseq
heatmap
updated 2 hours ago by
Ram
39k • written 2 hours ago by
ahmad mousavi
▴ 750
0
votes
1
reply
119
views
CIBERSORT Error: File not found
CIBERSORT
updated 15 hours ago by
ATpoint
72k • written 1 day ago by
jcara514
• 0
0
votes
1
reply
186
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 5 days ago by
raphael.B
▴ 360 • written 5 days ago by
sonsunjirachote
• 0
161 results • Page
2 of 4
Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
A: Finding zebrafish promoters ENSEMBL
Recent Locations •
All
United States,
just now
Boston,
2 minutes ago
Bologna,
3 minutes ago
Australia,
3 minutes ago
Texas, United States,
7 minutes ago
United States,
8 minutes ago
EU,
11 minutes ago
Recent Awards •
All
Scholar
to
Gordon Smyth
★ 6.1k
Scholar
to
GenoMax
130k
Popular Question
to
Payal
▴ 140
Scholar
to
nux
▴ 20
Scholar
to
Rory Stark
★ 1.8k
Supporter
to
Sasha
▴ 280
Popular Question
to
v.berriosfarias
▴ 100
Recent Replies
Comment: pal2nal -nogap -nomismatch options not working
by
Marie
• 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Arup Ghosh
3.2k
This post does not fit the theme of this forum.
Traffic: 2216 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6