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39 results • Page
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19
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11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 2 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 7 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
8
votes
16
replies
756
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 hour ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
4
votes
2
replies
366
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 16 hours ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
3
votes
3
replies
178
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 19 hours ago by
swbarnes2
14k • written 1 day ago by
M
• 0
3
votes
4
replies
232
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
22 hours ago by
QX
• 0
3
votes
0
replies
73
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
scRNA
Machinelearning
GenerativeAI
7 hours ago by
Claire Watson
▴ 60
3
votes
3
replies
119
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 5 hours ago by
GenoMax
141k • written 8 hours ago by
sapuizait
▴ 10
2
votes
5
replies
277
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
9 hours ago by
Lada
▴ 30
2
votes
1
reply
169
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 20 hours ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
2
votes
2
replies
158
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 5 hours ago by
dsull
★ 5.8k • written 12 hours ago by
Aaliya
▴ 10
2
votes
3
replies
318
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 4 hours ago by
dsull
★ 5.8k • written 17 days ago by
javanokendo
▴ 60
2
votes
4
replies
235
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 20 hours ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 21 hours ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
1
vote
1
reply
136
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 20 hours ago by
Ram
43k • written 1 day ago by
Francesco
▴ 10
1
vote
5
replies
215
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 2 hours ago by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
1
vote
0
replies
51
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
10 hours ago by
KABILAN
▴ 50
0
votes
0
replies
24
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
2 hours ago by
hagl
▴ 10
0
votes
7
replies
250
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 hour ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
0
votes
5
replies
244
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 1 hour ago by
Pierre Lindenbaum
161k • written 12 hours ago by
J
• 0
0
votes
0
replies
18
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 53 minutes ago by
Ram
43k • written 1 hour ago by
vanbelj
▴ 40
0
votes
2
replies
170
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 22 hours ago by
GenoMax
141k • written 1 day ago by
Begonia_pavonina
▴ 150
0
votes
0
replies
51
views
RNA-seq: full length gene
RNA-seq
updated 51 minutes ago by
Ram
43k • written 11 hours ago by
Nargis
• 0
0
votes
1
reply
112
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
AaronJaime
• 0
0
votes
0
replies
74
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 20 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
167
views
Highest variable features in single cell data
single-cell
updated 20 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
217
views
Annovar using R package
Annovar
gnomAD
R
20 hours ago by
DKA
▴ 40
0
votes
0
replies
112
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 20 hours ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
64
views
Designing single-stable RNA molecules
structure
RNA
20 hours ago by
Edna
• 0
0
votes
0
replies
76
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
20 hours ago by
simplitia
▴ 130
0
votes
2
replies
198
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 19 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
0
votes
11
replies
474
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
17 hours ago by
atowns21
• 0
0
votes
0
replies
47
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
13 hours ago by
turcoa1
• 0
0
votes
1
reply
79
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 12 hours ago by
Jeremy Leipzig
22k • written 13 hours ago by
zihanss
• 0
0
votes
0
replies
50
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
11 hours ago by
SineWave
• 0
0
votes
0
replies
70
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
8 hours ago by
HarperReed
• 0
0
votes
2
replies
205
views
PCA plot
DESeq2
PCAplot
updated 8 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
2
replies
146
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
7 hours ago by
The_PyPanda
▴ 10
0
votes
4
replies
343
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 2 hours ago by
pinheirofabiano
▴ 10 • written 3 days ago by
qudrat.nii
▴ 10
39 results • Page
1 of 1
Recent Votes
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: genome assembly records not present in assembly_summary.txt
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
A: How to process (seems) Agilent microarrry data?
Comment: genome assembly records not present in assembly_summary.txt
Answer: genome assembly records not present in assembly_summary.txt
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Recent Replies
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…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Answer: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
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