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121,965 results • Page
212 of 2440
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Votes
Replies
9
votes
8
replies
6.7k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 18 months ago by
Ram
45k • written 11.3 years ago by
Kizuna
▴ 880
5
votes
2
replies
1.4k
views
How to calculate GC content of reads that mapped to a specific gene?
STAR
RNA-seq
2.1 years ago by
bioinfo
▴ 160
41
votes
23
replies
45k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 3 months ago by
John Marshall
3.1k • written 4.2 years ago by
Michal Nevo
▴ 140
3
votes
5
replies
2.0k
views
Neither pysam nor samtools reading HTTPS-sourced BAM file correctly
bam
pysam
samtools
updated 2.1 years ago by
Istvan Albert
103k • written 2.1 years ago by
Alex Reynolds
36k
0
votes
1
reply
1.8k
views
computeMatrix error: [pyBwOpen] bw is NULL!
deeptools
bigWig
computeMatrix
updated 2.1 years ago by
rfran010
★ 1.6k • written 2.1 years ago by
bp22
▴ 80
0
votes
0
replies
953
views
getSex warning in minfi - what is the distinction between the two sex prediction methods?
methylation
ewas
minfi
2.1 years ago by
rkb965
• 0
0
votes
0
replies
495
views
BMIQ error: no-no missing arguments
methylation
ewas
wateRmelon
2.1 years ago by
rkb965
• 0
0
votes
2
replies
926
views
NCBI Genome Workbench Sequence ID edit
NCBI
Workbench
Genome
Sequence
2.1 years ago by
Paige
• 0
0
votes
4
replies
1.5k
views
Error using sequenza-utils with WES
WES
NGS
Sequenza
Sequenza-utils
2.1 years ago by
Camilo Andres
▴ 40
6
votes
10
replies
2.2k
views
Making pairwise matrix using ChIP-Seq peak binding matrix in R
R
matrix
binding
Chip-seq
2.1 years ago by
Ankit
▴ 520
3
votes
2
replies
943
views
Differential gene expression analysis after transcriptome assembly with SPAdes
SPAdes
differential-expression
transcriptome-assembly
updated 2.1 years ago by
Istvan Albert
103k • written 2.1 years ago by
langziv
▴ 70
0
votes
1
reply
1.2k
views
Meta analysis randon effects model and combined p-values
fisher
rma.uni
p-value
meta-analysis
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
mathias
• 0
0
votes
5
replies
1.4k
views
The effect of SNPs at the same location
genetics
updated 2.1 years ago by
LauferVA
4.8k • written 2.1 years ago by
Petras
• 0
1
vote
1
reply
780
views
ERROR Running EDTA
Transposon
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
manaswiniparija3
▴ 60
0
votes
0
replies
592
views
How Can I Identify Genes in the Top 100 Rank Space from SVD?
Singular-Value-Decomposition
Dimension-Reduction
SVD
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Raheleh
▴ 260
3
votes
2
replies
1.5k
views
How to download Time Calibration Data for Phylogenetic tree estimation ?
gene
DNA
RNA
updated 2.1 years ago by
Lada
▴ 40 • written 4.4 years ago by
sunnykevin97
▴ 1000
0
votes
1
reply
1.3k
views
Fossil calibration in PAML software?
Evolution
updated 2.1 years ago by
Lada
▴ 40 • written 6.2 years ago by
860101959
▴ 10
4
votes
7
replies
1.8k
views
How is the format of the bed file for samtools ampliconclip
samtools
ampliconclip
updated 2.1 years ago by
aw7
▴ 390 • written 2.1 years ago by
ManuelDB
▴ 110
0
votes
0
replies
562
views
Query Regarding Outlier Removal in RRBS Data Analysis Using MethylKit
rrbs
methylkit
epigenomics
2.1 years ago by
Srinka
▴ 20
3
votes
5
replies
1.7k
views
Optimal number of features to use when integrate multi samples by Seurat in scRNAseq
scRNASeq
Seurat
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
alwayshope
▴ 40
0
votes
1
reply
613
views
Filtered methylated sites annotation
methylation
annotation
TCGA
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
dilrajkaur766
• 0
7
votes
6
replies
2.3k
views
Best practices scRNA-seq guide for beginer
scRNA-seq
eBook
2.1 years ago by
octpus616
▴ 120
60
votes
21
replies
5.6k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 2.1 years ago by
Michael
56k • written 2.1 years ago by
sqshigg
▴ 60
0
votes
0
replies
885
views
News:
Online course: Easily analyze single cell RNA-seq data with Cellenics®, a user-friendly web-based platform
scRNA-seq
training
single-cell-RNA-seq
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Sara
• 0
6
votes
12
replies
7.9k
views
6 follow
Convert bed12 to GFF
bed
gff
bed12
5 months ago by
cmdcolin
★ 4.3k
0
votes
2
replies
1.8k
views
Why Beagle v5.4 fails during phasing large genotypic data set?
phasing
genotypes
beagle
updated 2.1 years ago by
4galaxy77
2.9k • written 2.1 years ago by
Famf
▴ 30
3
votes
2
replies
1.9k
views
import of HDF5 file into R
hdf5
2.1 years ago by
yueli7
▴ 250
0
votes
1
reply
915
views
Installing Galaxy
galaxy
sqlite3
updated 2.1 years ago by
GenoMax
154k • written 2.1 years ago by
GA
• 0
1
vote
6
replies
2.0k
views
Batch correction in DESeq2 - limited impact for unsupervised downstream analyses
deseq2
2.1 years ago by
Jane
• 0
12
votes
19
replies
15k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 19 months ago by
tiancheng
• 0 • written 3.3 years ago by
reany
▴ 50
0
votes
0
replies
605
views
What programs allow you to find the mutation rate of many sequences without needing to calculate by hand?
mutation-rate
SARS-CoV-2
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Madeline
• 0
7
votes
13
replies
3.7k
views
Help with Error: Required version of NumPy not available: installation of Numpy >= 1.6 not found
seurat
leiden
2.1 years ago by
Chris
▴ 360
3
votes
3
replies
1.9k
views
Annovar doesnt output CADD scores
Annovar
CADD
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
AMARU
• 0
0
votes
2
replies
1.6k
views
Error with galGal6 genome
karyoploter
R
karyoploteR
updated 2.1 years ago by
bernatgel
★ 3.4k • written 5.4 years ago by
palabari
▴ 10
1
vote
1
reply
857
views
Omics data and Mammography data repositories
repository
omics
mammography
updated 2.1 years ago by
aidangcruickshank
▴ 10 • written 2.1 years ago by
Ngrin
• 0
3
votes
2
replies
2.8k
views
Problems drawing cytobands with karyoploteR
RNA-Seq
R
Bioconductor
updated 2.1 years ago by
bernatgel
★ 3.4k • written 6.5 years ago by
uxiavb
▴ 10
0
votes
0
replies
745
views
News:
Join Our Online Course: Incorporating Paleogenomes into Evolutionary Genomics Studies
Paleogenomics
Genomics
aDNA
Adaptation-Genomics
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Physalia-courses
★ 2.6k
8
votes
9
replies
4.6k
views
What does a gene's "aligned length" represent?
alignment
2.1 years ago by
Ethan Lee
• 0
0
votes
1
reply
996
views
Biopython and Fab detection
biopython
fab-detection
antibody
updated 2.1 years ago by
Jesse
▴ 880 • written 2.1 years ago by
PamCraven
• 0
1
vote
4
replies
1.4k
views
How to understand if a GWAS sample comes from Chromosome X or Y
python
2.1 years ago by
dzisis1986
▴ 70
0
votes
0
replies
1.1k
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
Differential-expression
Normalization
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Sep
• 0
3
votes
7
replies
8.1k
views
6 follow
InferCNV results interpretation
cnv
scrna-seq
r
updated 15 months ago by
fxw193
• 0 • written 2.1 years ago by
fifty_fifty
▴ 90
0
votes
1
reply
530
views
FATAL ERROR on phASER
phASER
updated 2.1 years ago by
Pierre Lindenbaum
166k • written 2.1 years ago by
Shani
• 0
0
votes
0
replies
445
views
Differential expression between two different species tomato and pepper
Differential-expression
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Amior
• 0
2
votes
1
reply
1.3k
views
MAKER: how to use RNAseq data to assist annotation?
transcriptome
genome
MAKER
annotation
updated 2.1 years ago by
Juke34
9.3k • written 2.1 years ago by
bbscience
▴ 10
4
votes
12
replies
3.9k
views
bedops alternative for bedtools -unionbedg ?
bedtools
bam
coverage
bedops
bed
updated 2.1 years ago by
Alex Reynolds
36k • written 2.1 years ago by
Agastya
▴ 10
0
votes
1
reply
944
views
MAKER - How to set weight for merge legacy annotations
maker
annotation
updated 2.1 years ago by
Juke34
9.3k • written 2.1 years ago by
1300189805
• 0
1
vote
8
replies
3.8k
views
Negative Expression in RNA Assay on Dot Plot After SCT Transform
scttransform
scrnaseq
merge
Normalization
scaledata
updated 2.1 years ago by
fracarb8
★ 1.7k • written 2.1 years ago by
carolofharvest
▴ 50
0
votes
0
replies
680
views
How should I adjust covariates in eQTL analysis with an interaction term?
covariate
interaction
eQTL
2.1 years ago by
maximal_life
▴ 20
0
votes
0
replies
662
views
News:
Course on Phylogenomics
Phylogenetic-Inference
Divergence-Time-Estimation
Genomics
Phylogenomics
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Physalia-courses
★ 2.6k
121,965 results • Page
212 of 2440
Recent Votes
Answer: How to create a consensus of a contig with samtools or bbmap?
Comment: Getting just fastqc.zip file?
alternate allele frequency and minor allele frequency
Calculating minor allele frequency for GnomAD VCF file
Hiring FT Remote Nextflow engineer to build ML workflows for cancer genomics
Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
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arshad1292
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Comment: How to create a consensus of a contig with samtools or bbmap?
by
marongiu.luigi
▴ 760
sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon
by
V K
• 0
Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap?
by
lieven.sterck
16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants
by
benformatics
4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon
by
Mensur Dlakic
★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy
by
ATpoint
89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform)
by
rfran010
★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ?
by
Picasa
▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2
by
Olivia
• 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ?
by
GouthamAtla
12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
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