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33 results • Page
1 of 1
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19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 6 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 11 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
8
votes
16
replies
783
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 5 hours ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
4
votes
2
replies
368
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 20 hours ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
3
votes
3
replies
148
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 9 hours ago by
GenoMax
141k • written 12 hours ago by
sapuizait
▴ 10
3
votes
0
replies
85
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 10 minutes ago by
Ram
43k • written 10 hours ago by
Claire Watson
▴ 60
3
votes
3
replies
186
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 23 hours ago by
swbarnes2
14k • written 1 day ago by
M
• 0
2
votes
5
replies
279
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
13 hours ago by
Lada
▴ 30
2
votes
3
replies
222
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 1 hour ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
2
votes
2
replies
174
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 9 hours ago by
dsull
★ 5.8k • written 15 hours ago by
Aaliya
▴ 10
2
votes
3
replies
319
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 7 hours ago by
dsull
★ 5.8k • written 17 days ago by
javanokendo
▴ 60
1
vote
0
replies
56
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
14 hours ago by
KABILAN
▴ 50
1
vote
5
replies
241
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 6 hours ago by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
1
vote
2
replies
221
views
PCA plot
DESeq2
PCAplot
updated 11 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
6
replies
380
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 22 minutes ago by
GenoMax
141k • written 3 days ago by
qudrat.nii
▴ 10
0
votes
0
replies
10
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
14 minutes ago by
pairedttest
▴ 10
0
votes
3
replies
179
views
Highest variable features in single cell data
single-cell
updated 20 minutes ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
157
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 10 minutes ago by
Ram
43k • written 22 hours ago by
The_PyPanda
▴ 10
0
votes
0
replies
70
views
Designing single-stable RNA molecules
structure
RNA
23 hours ago by
Edna
• 0
0
votes
0
replies
57
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 14 minutes ago by
Ram
43k • written 14 hours ago by
SineWave
• 0
0
votes
0
replies
81
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
23 hours ago by
simplitia
▴ 130
0
votes
2
replies
204
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 23 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
0
votes
11
replies
477
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
20 hours ago by
atowns21
• 0
0
votes
0
replies
54
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
16 hours ago by
turcoa1
• 0
0
votes
1
reply
88
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 16 hours ago by
Jeremy Leipzig
22k • written 16 hours ago by
zihanss
• 0
0
votes
0
replies
79
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
11 hours ago by
HarperReed
• 0
0
votes
7
replies
279
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 5 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
0
votes
5
replies
272
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 4 hours ago by
Pierre Lindenbaum
161k • written 16 hours ago by
J
• 0
0
votes
0
replies
41
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 hours ago by
Ram
43k • written 5 hours ago by
vanbelj
▴ 40
0
votes
0
replies
59
views
RNA-seq: full length gene
RNA-seq
updated 4 hours ago by
Ram
43k • written 15 hours ago by
Nargis
• 0
0
votes
0
replies
41
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 3 hours ago by
GenoMax
141k • written 6 hours ago by
hagl
▴ 10
0
votes
1
reply
58
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
chaco001
▴ 40
0
votes
0
replies
28
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 1 hour ago by
Ram
43k • written 2 hours ago by
Guille
• 0
33 results • Page
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Recent Votes
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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Recent Replies
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
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