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117,010 results • Page
4 of 2341
Sort: Rank
Rank
Views
Votes
Replies
2
votes
5
replies
597
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 6 days ago by
arctic
▴ 40 • written 16 days ago by
M.
▴ 30
1
vote
2
replies
363
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 6 days ago by
Ram
43k • written 7 days ago by
t.fortunato.asquini
• 0
2
votes
1
reply
265
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 7 days ago by
pjb39
▴ 210 • written 8 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
215
views
Output file of samtools flagstat empty
samtools-flagstat
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
ramendra.sarma
• 0
2
votes
8
replies
388
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 7 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
130
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
7 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
237
views
input file in rmats
rmats
updated 7 days ago by
Mathew
▴ 140 • written 9 days ago by
Lambodarswain316
• 0
3
votes
3
replies
368
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 5 days ago by
Mathew
▴ 140 • written 8 days ago by
Christopher
• 0
6
votes
7
replies
395
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
6 days ago by
sansan_96
▴ 90
2
votes
3
replies
291
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
6 days ago by
Azra
▴ 10
2
votes
1
reply
234
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 8 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 8 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
6 days ago by
beginner123
• 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 8 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
0
votes
2
replies
235
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
6 days ago by
analyst
▴ 50
0
votes
6
replies
428
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 5 days ago by
Ram
43k • written 8 days ago by
ajbarrett98
• 0
0
votes
11
replies
553
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
6 days ago by
Tuck898
• 0
3
votes
3
replies
287
views
what is another word for a BLAST "hit"?
blast
alignment
8 days ago by
dec986
▴ 380
0
votes
1
reply
207
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 8 days ago by
Ram
43k • written 8 days ago by
Shwetha
• 0
0
votes
0
replies
165
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 8 days ago by
Ram
43k • written 9 days ago by
naomiboldon
• 0
1
vote
3
replies
294
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 8 days ago by
Ram
43k • written 9 days ago by
Omics data mining
▴ 260
9
votes
6
replies
12k
views
samtools tview symbols
samtools
updated 8.8 years ago by
Ashutosh Pandey
12k • written 8.8 years ago by
biolab
★ 1.4k
2
votes
9
replies
725
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 12 days ago by
schmince
• 0
0
votes
5
replies
326
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
6 days ago by
SilhouetteQ
• 0
0
votes
1
reply
197
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 9 days ago by
GenoMax
142k • written 9 days ago by
maria.soler
• 0
0
votes
2
replies
301
views
How are score_weights calculated in this code?
single-cell
8 days ago by
carolofharvest
▴ 40
0
votes
1
reply
228
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 8 days ago by
curious
▴ 750 • written 9 days ago by
SeoGyun
• 0
0
votes
0
replies
157
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
9 days ago by
Samantha
• 0
0
votes
1
reply
194
views
Microbial Signal Transduction Database
MiST
updated 9 days ago by
zx8754
11k • written 9 days ago by
Shravani
• 0
1
vote
1
reply
223
views
DESeq2 error
DESeq2
updated 9 days ago by
ATpoint
82k • written 9 days ago by
sooni
▴ 20
0
votes
0
replies
145
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
9 days ago by
singcell
• 0
0
votes
1
reply
220
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 9 days ago by
ATpoint
82k • written 9 days ago by
Amr
▴ 160
0
votes
2
replies
235
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
9 days ago by
jain72744
▴ 10
6
votes
2
replies
244
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 9 days ago by
Gordon Smyth
★ 7.2k • written 9 days ago by
gBioStar5
▴ 10
2
votes
5
replies
414
views
Importing a fastq file
Fastq
updated 9 days ago by
size_t
▴ 120 • written 10 days ago by
oumo
• 0
3
votes
1
reply
209
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 9 days ago by
dthorbur
★ 2.0k • written 9 days ago by
Eren
• 0
0
votes
0
replies
158
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
9 days ago by
Aytaç
• 0
0
votes
0
replies
171
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 9 days ago by
zx8754
11k • written 9 days ago by
curious_butterfly
• 0
0
votes
0
replies
165
views
supervised admixture
supervised
admixture
9 days ago by
RT
▴ 10
2
votes
0
replies
158
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
9 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
464
views
Different output for read length
samtools
BAM
9 days ago by
marco.barr
▴ 130
0
votes
1
reply
369
views
Snakemake fails to find conda in PBS
snakemake
updated 9 days ago by
tim.booth
▴ 60 • written 5 weeks ago by
yixinzeng
• 0
0
votes
2
replies
231
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 8 days ago by
Ram
43k • written 10 days ago by
sainavyav22
• 0
3
votes
4
replies
330
views
Truncated metadata file report from ENA Portal API
ena
python
8 days ago by
Giulia
• 0
0
votes
0
replies
189
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
10 days ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
570
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 10 days ago by
Ram
43k • written 12 weeks ago by
maplewj
▴ 10
0
votes
5
replies
340
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
6 days ago by
feather-W
• 0
0
votes
3
replies
306
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 10 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
Matthew
• 0
3
votes
4
replies
3.0k
views
Have you ever obtained user guide of ExomeCNV?
CNV
updated 4.4 years ago by
lffu_0032
▴ 90 • written 5.2 years ago by
oghzzang
▴ 50
0
votes
1
reply
157
views
input file for alternative splicing in rmats in linux
rmats
updated 10 days ago by
Ram
43k • written 10 days ago by
Lambodarswain316
• 0
117,010 results • Page
4 of 2341
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
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constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
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• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
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marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
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ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
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I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
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Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
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Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
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Fixed the issue by updating nucmer version.
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142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
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you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
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What is your question? It's unclear.
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One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
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See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
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