Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
181 results • Page
2 of 4
Sort: Views
Rank
Views
Votes
Replies
2
votes
3
replies
312
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 3 days ago by
bk11
★ 2.4k • written 7 days ago by
Yoosef
▴ 60
0
votes
6
replies
308
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 5 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
ajbarrett98
• 0
1
vote
4
replies
303
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
2 days ago by
rackbersingh
• 0
10
votes
3
replies
301
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 4 days ago by
b.contreras.moreira
▴ 180 • written 5 days ago by
ijarne
• 0
0
votes
1
reply
301
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 6 days ago by
aaron.stevens
• 0 • written 3 months ago by
sativus
▴ 20
1
vote
3
replies
299
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
6 days ago by
Dora
▴ 10
0
votes
5
replies
290
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
4 days ago by
me
• 0
3
votes
4
replies
288
views
Truncated metadata file report from ENA Portal API
ena
python
2 days ago by
Giulia
• 0
0
votes
1
reply
287
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 5 days ago by
andres.firrincieli
3.6k • written 6 days ago by
Antonio
• 0
5
votes
5
replies
281
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
4 days ago by
Chris
▴ 280
0
votes
3
replies
280
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Matthew
• 0
0
votes
2
replies
272
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 6 days ago by
GenoMax
142k • written 7 days ago by
mropri
▴ 150
0
votes
4
replies
268
views
Correlation Analysis
statistics
methylation
NGS
expression
1 day ago by
Researcher
▴ 30
0
votes
1
reply
265
views
creating batch colum for batch correction
batch-correction
combat
6 days ago by
Expert
▴ 10
1
vote
1
reply
265
views
Seurat V5 integration
Seurat
integration
updated 4 days ago by
Ram
43k • written 7 days ago by
starswillfade
▴ 10
6
votes
7
replies
264
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
3 hours ago by
sansan_96
▴ 90
1
vote
2
replies
259
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 5 days ago by
Weiwen
• 0 • written 6 days ago by
MICOS
▴ 10
0
votes
2
replies
257
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 2 days ago by
GenoMax
142k • written 9 days ago by
Ximena
• 0
0
votes
2
replies
257
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
5 days ago by
sainavyav22
• 0
0
votes
5
replies
256
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
2 days ago by
SilhouetteQ
• 0
4
votes
2
replies
253
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
3 days ago by
mnx0723
• 0
0
votes
2
replies
250
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 5 days ago by
Xiaofen
• 0 • written 5 days ago by
toddknutson
▴ 60
0
votes
2
replies
243
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated just now by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
yahn
• 0
1
vote
3
replies
247
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
Ngrin
• 0
0
votes
1
reply
245
views
barcode of TCR-sequencing
barcode
updated 4 days ago by
mizraelson
▴ 60 • written 12 days ago by
yueli7
▴ 250
3
votes
3
replies
245
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
5 days ago by
Adyasha
• 0
0
votes
1
reply
244
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Sony
▴ 10
4
votes
1
reply
244
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 6 days ago by
zx8754
11k • written 8 days ago by
Jautis
▴ 560
0
votes
2
replies
241
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
5 days ago by
Ahiad Chen Zion
• 0
0
votes
2
replies
240
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Prawesh
• 0
0
votes
5
replies
240
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 4 days ago by
Joe
21k • written 4 days ago by
Lemonhope
• 0
0
votes
2
replies
240
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
6 days ago by
kalavattam
▴ 190
1
vote
2
replies
236
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 6 days ago by
zx8754
11k • written 6 days ago by
snajafy
• 0
0
votes
3
replies
235
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
updated 3 days ago by
Ram
43k • written 3 days ago by
feather-W
• 0
0
votes
2
replies
231
views
How are score_weights calculated in this code?
single-cell
1 day ago by
carolofharvest
▴ 40
1
vote
3
replies
231
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 3 days ago by
GenoMax
142k • written 4 days ago by
cput
• 0
0
votes
3
replies
227
views
STAR aligner error
RNA-seq
STAR
slurm
updated 4 days ago by
Ram
43k • written 5 days ago by
M.
▴ 30
1
vote
3
replies
226
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 2 days ago by
Ram
43k • written 2 days ago by
Omics data mining
▴ 260
0
votes
3
replies
223
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
updated 10 minutes ago by
fracarb8
★ 1.6k • written 1 day ago by
beginner123
• 0
2
votes
8
replies
224
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 8 hours ago by
Pierre Lindenbaum
161k • written 12 hours ago by
Matteo Ungaro
▴ 100
0
votes
2
replies
217
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 4 days ago by
Ram
43k • written 4 days ago by
Sumeet
• 0
1
vote
2
replies
216
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 3 days ago by
Michael
54k • written 3 days ago by
ashaneev07
▴ 20
1
vote
1
reply
215
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 5 days ago by
Michael
54k • written 6 days ago by
Guillermo
• 0
0
votes
2
replies
211
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
ahmad.sajad4541
• 0
3
votes
3
replies
207
views
what is another word for a BLAST "hit"?
blast
alignment
2 days ago by
dec986
▴ 380
0
votes
2
replies
207
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 2 days ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
1
vote
1
reply
206
views
Gene ontology and homologs
gene-ontology
updated 6 days ago by
geneontologyhelp
▴ 400 • written 7 days ago by
beshka194
• 0
1
vote
2
replies
205
views
Genome Assembly task + Protein Translation, assignment advice on a question
sequence-analysis
protein-synthesis
1 day ago by
rackbersingh
• 0
2
votes
3
replies
204
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
ScottDansk
▴ 10
6
votes
2
replies
196
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 2 days ago by
Gordon Smyth
★ 7.1k • written 2 days ago by
gBioStar5
▴ 10
181 results • Page
2 of 4
Recent Votes
Answer: How to compute TPM normalized values for TCGA miRNA data?
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
Answer: install package
Answer: How I do lift over a Plink bim file from Hg18 to Hg19.
Answer: joint callset and vcf sorting, unknown TAG issue
Recent Locations •
All
United States,
2 minutes ago
United States,
9 minutes ago
Brazil,
11 minutes ago
Russia,
11 minutes ago
France,
13 minutes ago
Oviedo,
17 minutes ago
Russia,
26 minutes ago
Recent Awards •
All
Popular Question
to
rj.rezwan
• 0
Scholar
to
colindaven
6.4k
Scholar
to
pjb39
▴ 200
Popular Question
to
Jen
▴ 70
Scholar
to
Pierre Lindenbaum
161k
Popular Question
to
Michael
54k
Popular Question
to
Kai_Qi
▴ 130
Recent Replies
Comment: Extracting mutation status from MAF files - TCGA
by
Zhenyu Zhang
★ 1.2k
you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38
by
Zhenyu Zhang
★ 1.2k
Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
Answer: Nomalization - TCGA, RNA-seq and Microarray
by
Zhenyu Zhang
★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
by
ATpoint
82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the R verison you are using (or packages it depends on) are not compatible with the R version you are using any…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
▴ 100
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2
by
BioinfGuru
★ 1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
Traffic: 1311 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6