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185 results • Page
2 of 4
Sort: replies
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0
votes
4
replies
523
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 5 days ago by
ATpoint
82k • written 6 days ago by
rheab1230
▴ 140
0
votes
4
replies
250
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
0
votes
4
replies
347
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 3 hours ago by
pinheirofabiano
▴ 10 • written 3 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
284
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
dxj294
• 0
2
votes
3
replies
946
views
Method to detect genome doubling
CNV
genome doubling
updated 4 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
3
replies
289
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 3 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
emmanouil.a
▴ 120
3
votes
3
replies
193
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
c_u
▴ 520
3
votes
3
replies
717
views
KissDE and batch effect
kissDE
kissplice
4 days ago by
david.b.rombaut
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
3
replies
197
views
from row count to tpm
tpm
row-count
normalization
3 days ago by
michelafrancesconi9
▴ 20
0
votes
3
replies
483
views
python file for coding potential calculator
cpc2.py
updated 3 days ago by
atharvakarkare14
▴ 10 • written 7 days ago by
Ashok
• 0
1
vote
3
replies
209
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 1 day ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
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
0
votes
3
replies
367
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 3 days ago by
colindaven
6.4k • written 11 days ago by
rj.rezwan
• 0
0
votes
3
replies
209
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 3 days ago by
mchour
• 0 • written 3 days ago by
rhossen
• 0
2
votes
3
replies
201
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
analyst
▴ 30
3
votes
3
replies
470
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
6
votes
3
replies
180
views
Interpretting IGV output
IGV
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
analyst
▴ 30
3
votes
3
replies
125
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 5 hours ago by
GenoMax
141k • written 9 hours ago by
sapuizait
▴ 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
3
votes
3
replies
221
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Estevão
• 0
0
votes
3
replies
235
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 2 days ago by
Istvan Albert
100k • written 3 days ago by
Dylan
• 0
1
vote
3
replies
250
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
3
votes
3
replies
218
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Mariana
▴ 10
0
votes
2
replies
798
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 2 days ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
2
replies
581
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 1 day ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
0
votes
2
replies
148
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
7 hours ago by
The_PyPanda
▴ 10
0
votes
2
replies
213
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
2 days ago by
mropri
▴ 150
2
votes
2
replies
202
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 2 days ago by
analyst
▴ 30 • written 2 days ago by
lorena9132
• 0
0
votes
2
replies
260
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
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
2
replies
175
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
3 days ago by
sainavyav22
• 0
2
votes
2
replies
161
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 6 hours ago by
dsull
★ 5.8k • written 12 hours ago by
Aaliya
▴ 10
0
votes
2
replies
217
views
Annovar using R package
Annovar
gnomAD
R
21 hours ago by
DKA
▴ 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
1
vote
2
replies
200
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
2
replies
167
views
Highest variable features in single cell data
single-cell
updated 21 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
7
votes
2
replies
263
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 2 days ago by
geneontologyhelp
▴ 390 • written 4 days ago by
catherine.teyssier
• 0
3
votes
2
replies
271
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
4 days ago by
kristiewyleung
• 0
0
votes
2
replies
192
views
Result of running of p3_in.pl
primer3
updated 4 days ago by
GenoMax
141k • written 4 days ago by
nasri
• 0
1
vote
2
replies
233
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 18 days ago by
Netanel
• 0
0
votes
2
replies
237
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
0
votes
2
replies
200
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
biochugs
• 0
4
votes
2
replies
367
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 16 hours ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 1 day ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
0
votes
2
replies
205
views
PCA plot
DESeq2
PCAplot
updated 8 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
2
votes
2
replies
418
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 3 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
132
views
Plots for DNA methylation data
plots
DNA
methylation
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sarahawan92
▴ 10
2
votes
1
reply
286
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 6 days ago by
GenoMax
141k • written 6 days ago by
rebecca.calvo
• 0
185 results • Page
2 of 4
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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