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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
177
views
selection of 2 by 2 Chi-square Test
statistics
Chi-square
updated 4 days ago by
Ram
38k • written 4 days ago by
Binghong
▴ 20
0
votes
0
replies
180
views
Check most expressed isoform of mouse gene in specific tissue
FANTOM
gene-expression
MGI
mouse
updated 4 days ago by
Ram
38k • written 4 days ago by
gspirito
▴ 10
1
vote
0
replies
176
views
gseKEGG with streptomyces coelicolor - No gene can be mapped
streptomyces
KEGG
clusterProfiler
4 days ago by
r.evans2
▴ 10
0
votes
0
replies
242
views
Power calculations for the detection of differentially expressed genes in pseudobulk scRNA-seq data
scRNA-seq
pseudobulk
power
RNA-seq
updated 4 days ago by
Ram
38k • written 4 days ago by
Ali
• 0
2
votes
8
replies
465
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools
depth-of-coverage
Mitochondrial-genome
2 days ago by
Lida
• 0
0
votes
1
reply
205
views
Genes near SNP within certain window frame and distance
bedops
bedtools
updated 4 days ago by
Ram
38k • written 4 days ago by
waqaskhokhar999
▴ 150
0
votes
0
replies
191
views
95% CI for AUC in R
AUC
R
4 days ago by
dhananya
• 0
0
votes
1
reply
239
views
comparison between STARsolo and cellranger
STARsolo
cellranger
updated 4 days ago by
GenoMax
126k • written 4 days ago by
dalibenam64
• 0
0
votes
1
reply
186
views
building model with lectin array data and patient data
lectin
model
updated 4 days ago by
ATpoint
70k • written 4 days ago by
dharmini1998
• 0
1
vote
1
reply
204
views
What's the correct way to map to hg38 with alternative contigs?
NGS
bwa
updated 4 days ago by
ATpoint
70k • written 4 days ago by
Belanov
▴ 10
0
votes
0
replies
191
views
How to find association between a gene-rsid and AD
association
Loci
LD
AD
4 days ago by
rheab1230
▴ 140
0
votes
2
replies
249
views
Finding repeats in dna sequences
OP
4 days ago by
ojaswinipandey
• 0
0
votes
0
replies
184
views
Why DEG analysis of the same region in two different datasets results in different sets of DEGs?
single
integration
cell
DEG
design
analysis
5 days ago by
paria
▴ 70
1
vote
0
replies
148
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
4 days ago by
Hyper_Odin
▴ 280
0
votes
0
replies
120
views
Metatranscriptomics: de novo assembly of mRNA per OTU?
MAGs
no
total
novo
metatranscriptomics
assembly
de
MEGAN
rna
5 days ago by
Maria
• 0
0
votes
3
replies
152
views
A problem about saving Rstudio data matrix
data
Rstudio
matrix
updated 5 days ago by
bkleiboeker
▴ 320 • written 5 days ago by
yoser4
▴ 10
0
votes
0
replies
82
views
How can I obtain the significantly different taxa data from this Aldex plot ? (Using R)
taxa
test
Aldex2
of
abundance
Relative
R
5 days ago by
ohtang7
▴ 30
0
votes
0
replies
106
views
GO analysis in R vs website
GO
5 days ago by
Thomas
• 0
0
votes
0
replies
92
views
Observed vs. expected occurences in genomic windows
ngs
statistics
snp
5 days ago by
schmau
▴ 10
0
votes
0
replies
101
views
How generate sample sheet data for Illumina Infinium Global Screening Array *.idat file?
Global
microarray
Illumina
Infinium
Screening
.idat
Array
5 days ago by
Jichen Wen
▴ 30
0
votes
1
reply
172
views
Combining RNAseq datasets
RNAseq
DEseq
NGS
updated 5 days ago by
rpolicastro
11k • written 5 days ago by
torio
• 0
0
votes
2
replies
204
views
Do we need replicates for PSI calculation in SUPPA2?
SUPPA2
splicing
RNA-seq
Alternative
5 days ago by
sreelekha
▴ 10
0
votes
0
replies
168
views
How to export the result contents (analyzed part only) of clr function to the CSV file ? (The microbiota data) in R Aldex2 package
Aldex2
ASV
R
updated 4 days ago by
Ram
38k • written 5 days ago by
ohtang7
▴ 30
0
votes
0
replies
125
views
check if a protein abundance is expected to be low
mass-spectrometry
5 days ago by
Abhishek
• 0
0
votes
0
replies
108
views
Error when trying to send data to DB chado
install
chado
error
5 days ago by
Marcos
▴ 10
0
votes
0
replies
137
views
Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq
genomics
star
fastq
alignment
5 days ago by
O.rka
▴ 650
0
votes
0
replies
141
views
inquiry related to same SNP for a gene across for two tissues
snp
relation
tissue
genetics
gene
5 days ago by
rheab1230
▴ 140
6
votes
11
replies
675
views
Calculate RPKM
RPKM
14 hours ago by
Chris
▴ 70
0
votes
0
replies
115
views
chia-pet tutorial
snp
gene
chia-pet
5 days ago by
rheab1230
▴ 140
0
votes
0
replies
132
views
DESeq2 for time series and control-treated groups
log2foldchange
DESeq2
6 days ago by
t.ru
• 0
2
votes
3
replies
251
views
mRNA Seq
NGS
updated 4 days ago by
Ram
38k • written 6 days ago by
Yaseen
▴ 10
0
votes
0
replies
114
views
Adding MBC/UMI RX tag to read name
umi
6 days ago by
Christian
▴ 20
1
vote
7
replies
240
views
error bbduk
linux
bbduk
java
updated 6 days ago by
lieven.sterck
14k • written 6 days ago by
Kárita
• 0
0
votes
0
replies
100
views
Seeking explanation of the difference between GO term normal vs non-redundant!
GO
RNA-seq
term
analysis
webgestalt
6 days ago by
Soumajit
▴ 30
0
votes
2
replies
193
views
Xenocell - Error in classify reads
Xenocell
PDX
scRNAseq
singularity-container
5 days ago by
c2e09af0
• 0
0
votes
0
replies
139
views
How to detect tumor-specific splicing aberrations
splicing
6 days ago by
iraun
5.8k
1
vote
1
reply
194
views
From where i can download the bed file of hg19 which contaning the corrdinates as well as gene name.
bed
updated 4 days ago by
Ram
38k • written 6 days ago by
Anisha
• 0
0
votes
2
replies
228
views
Databases for cell lines
Genomics
Genetics
updated 4 days ago by
Ram
38k • written 7 days ago by
aranyak111
• 0
0
votes
0
replies
129
views
Exomedepth Correlation <97 in X chromosome
exomedepth
7 days ago by
Gerardo
• 0
0
votes
1
reply
197
views
Chiseq files for deseq2
countMatrix
deseq2
Chipseq
updated 7 days ago by
Darked89
4.2k • written 7 days ago by
Chava-Lea
• 0
1
vote
2
replies
225
views
RNA-seq data analysis (prokaryotes) featurecounts with
featureCounts
RNA-Seq
7 days ago by
Pegasus
▴ 80
0
votes
1
reply
359
views
Using Arriba for gene fusion? chimOutTyp SeparateSAMMold of star not working
Fusion
RNASeq
updated 7 days ago by
nicolas.ares
• 0 • written 13 months ago by
Claire
• 0
0
votes
0
replies
116
views
Problem with homer in findMotifs.pl when using input and bg fasta
motif
Homer
findMotifs.pl
updated 7 days ago by
GenoMax
126k • written 7 days ago by
Ilario
• 0
0
votes
3
replies
317
views
Alt allele - after bcftools norm
bcftools
GATK
VCF
updated 6 days ago by
iraun
5.8k • written 7 days ago by
kamanovae
▴ 80
1
vote
2
replies
266
views
How to get rid of all copies of repeated lines in BLAST result text files
BLASTX
Python
BLAST
6 days ago by
Hau
• 0
0
votes
0
replies
166
views
Diamond blast functional annotation
blast
Diamond
updated 7 days ago by
Ram
38k • written 7 days ago by
hellokwmin
• 0
0
votes
0
replies
141
views
Stage 8 error on Desmond
Maestro
Molecular-Simulation
Desmond
Schrodinger
updated 7 days ago by
Ram
38k • written 7 days ago by
bhavya2269
• 0
0
votes
1
reply
193
views
Parser EggNOG-mapper annotation output using pythom
EggNOG-mapper
Python
updated 7 days ago by
Mensur Dlakic
★ 23k • written 7 days ago by
ben@f
• 0
1
vote
2
replies
285
views
Bioinformatics package
python
updated 6 days ago by
WouterDeCoster
47k • written 7 days ago by
zainabi8077
▴ 10
0
votes
0
replies
150
views
ATAC seq fragment file
ATAC-seq
updated 8 days ago by
Ram
38k • written 8 days ago by
Chris
▴ 70
1,000 results • Page
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Recent Votes
Visualization of RNA editing on a gene - What is the best way and tool/plot that can be used?
Creating sample groups from a combination of genes for survival analysis
A: Visualization for ChIP-seq analysis
ChIP-seq analysis: Tutorial for Beginners
Answer: wrong quality plots in fastqc output
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
Comment: Power analysis for patient samples
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Recent Awards •
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Scholar
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GenoMax
126k
Popular Question
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shpak.max
▴ 20
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hugo.avila
▴ 490
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Recent Replies
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
GenoMax
126k
> I can't find the way using the man documentation of bcftools to get a > .vcf from a sorted .bam file. This should be all you need: https…
Comment: RNA-SEQ
by
Trivas
▴ 630
You should be able to do `fasterq-dump <SRR number> -O output_folder`
Comment: RNA-SEQ
by
GenoMax
126k
If you are trying to re-create an analysis and if it used both SRA# then you will need to get both. If you are simply learning/testing then…
Comment: wrong quality plots in fastqc output
by
poecile.pal
▴ 50
I understood why I got high percentage of duplication. The size of reference was about 150K bp, while I asked for 30M reads with length 151…
Comment: RNA-SEQ
by
ali
• 0
so if I just consider one of the SRR and use fastq-dump --splite -files , its okay ???
Comment: Creating a loop to mark duplicates using Picard
by
Ram
38k
> don't use a loop in a script shell when you can use Snakemake or Nextflow People need to start somewhere. Loops -> xargs/parallel -> sna…
Comment: Mapping paired end reads with ngm and samtools, using prefixes and suffixes for
by
Ram
38k
> what should be the smpl_names.txt That's the file name for the output. Learn more about redirection in linux - Google the term. And yes,…
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
by
Trivas
▴ 630
First, set `show_row_names = FALSE`. You might want to play around with the `col = col_fun` portion of the vignette to change your scale to…
Answer: RNA-SEQ
by
Trivas
▴ 630
Those are replicates, and if you download the SRR files, you should automatically get R1 and R2 for each SRR.
Answer: Creating a loop to mark duplicates using Picard
by
Pierre Lindenbaum
153k
METRICS_FILE="$sbam"/"${bamfile%_sorted.bam}"_metrix instead of METRICS_FILE="$sbam"/"${sbam%_sorted.bam}"_metrix also check the…
Answer: known-sites for Felis_catus_9.0 (GCA_000181335.4)
by
Pierre Lindenbaum
153k
https://ftp.ensembl.org/pub/release-109/variation/gvf/felis_catus/
Comment: Power analysis for patient samples
by
aropri
▴ 120
Sounds good, thanks Jeremy for the help, really appreciate it.
Comment: Power analysis for patient samples
by
Jeremy
▴ 760
I think you're doing it right. Since you only have 2 groups, you can use `pwr.t.test`. The default alternative hypothesis is two-sided, b…
Answer: Active enhancers for mm39
by
LChart
2.1k
Ensembl has a regulatory build for GRCm39: https://ftp.ensembl.org/pub/current_regulation/mus_musculus/ Note that the elements are de…
Comment: Active enhancers for mm39
by
Matthias Zepper
3.4k
Wouldn't [liftOver][1] be an option to remap the coordinates to the new assembly? E.g. the [mm10 to mm39][2] chain? [1]: http://hgdownl…
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