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390 results • Page
4 of 8
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Views
Votes
Replies
1
vote
3
replies
308
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 13 days ago by
GenoMax
142k • written 13 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
307
views
RNAseq 1 control 2 different treatment
RNA-seq
27 days ago by
matteo.levorato
• 0
0
votes
3
replies
307
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 13 days ago by
GenoMax
142k • written 14 days ago by
kim
• 0
1
vote
3
replies
306
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
8 days ago by
Lada
▴ 30
3
votes
5
replies
306
views
Generating mpileup file using samtools
mpileup
samtools
updated 10 days ago by
Joe
21k • written 10 days ago by
Ruqaiya
• 0
2
votes
3
replies
305
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 10 days ago by
dthorbur
★ 2.0k • written 10 days ago by
Vijith
▴ 30
2
votes
2
replies
303
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
28 days ago by
bioinfo
▴ 150
0
votes
2
replies
303
views
Annovar using R package
Annovar
gnomAD
R
18 days ago by
DKA
▴ 40
0
votes
1
reply
302
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 26 days ago by
GenoMax
142k • written 26 days ago by
ycts
• 0
0
votes
2
replies
299
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 27 days ago by
Ram
43k • written 27 days ago by
David
• 0
0
votes
2
replies
297
views
Bedmethyl file format
bedmethyl
methylation
updated 26 days ago by
GenoMax
142k • written 26 days ago by
njornet
▴ 20
0
votes
1
reply
296
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 24 days ago by
GenoMax
142k • written 24 days ago by
bioyas
▴ 10
0
votes
2
replies
295
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
26 days ago by
DKA
▴ 40
3
votes
4
replies
294
views
Truncated metadata file report from ENA Portal API
ena
python
3 days ago by
Giulia
• 0
1
vote
2
replies
293
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 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
0
votes
2
replies
292
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
26 days ago by
mropri
▴ 150
0
votes
5
replies
291
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
9 hours ago by
SilhouetteQ
• 0
1
vote
3
replies
290
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
20 days ago by
WouterDeCoster
47k
0
votes
1
reply
290
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 6 days ago by
andres.firrincieli
3.6k • written 7 days ago by
Antonio
• 0
5
votes
5
replies
289
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
5 days ago by
Chris
▴ 280
0
votes
4
replies
285
views
Genbank File Format
gbkformat
13 days ago by
alenew.am
• 0
0
votes
2
replies
283
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 23 hours ago by
Zhenyu Zhang
★ 1.2k • written 10 days ago by
yahn
• 0
0
votes
0
replies
283
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 21 days ago by
Ram
43k • written 14 months ago by
Pine
▴ 20
0
votes
1
reply
279
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 28 days ago by
GenoMax
142k • written 28 days ago by
haiying.kong
▴ 360
0
votes
4
replies
276
views
Correlation Analysis
statistics
methylation
NGS
expression
2 days ago by
Researcher
▴ 30
1
vote
2
replies
274
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
11 days ago by
rianna.collins
• 0
1
vote
2
replies
273
views
alignment result
RNA-seq
samtools
hisat2
18 days ago by
ahmad.sajad4541
• 0
1
vote
2
replies
273
views
permutation test in edgeR
rna-seq
edgeR
updated 21 days ago by
Gordon Smyth
★ 7.1k • written 5 weeks ago by
Netanel
• 0
0
votes
2
replies
266
views
Downloading older version of a tool
Alignment
tools
9 days ago by
Ruqaiya
• 0
0
votes
1
reply
266
views
creating batch colum for batch correction
batch-correction
combat
7 days ago by
Expert
▴ 10
0
votes
2
replies
265
views
How are score_weights calculated in this code?
single-cell
2 days ago by
carolofharvest
▴ 40
1
vote
3
replies
263
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 3 days ago by
Ram
43k • written 3 days ago by
Omics data mining
▴ 260
1
vote
3
replies
261
views
Odd alignment question/finding
Alignment
updated 10 days ago by
barslmn
★ 2.1k • written 11 days ago by
poordumbsillyidiot
• 0
1
vote
1
reply
260
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 18 days ago by
ATpoint
82k • written 18 days ago by
AaronJaime
• 0
0
votes
2
replies
260
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
6 days ago by
sainavyav22
• 0
0
votes
2
replies
259
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 10 days ago by
Ximena
• 0
1
vote
2
replies
258
views
Downloading full alignments from Pfam
pfam
8 days ago by
bef1
• 0
0
votes
0
replies
256
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
14 days ago by
SSSJec
• 0
1
vote
1
reply
253
views
Retrieve a % coverage for each transcript
RNA-seq
updated 26 days ago by
Ram
43k • written 26 days ago by
jammydodger123456
▴ 40
0
votes
5
replies
251
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 5 days ago by
Joe
21k • written 5 days ago by
Lemonhope
• 0
1
vote
1
reply
250
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 13 days ago by
Ram
43k • written 13 days ago by
Jonathan Yoou
▴ 60
3
votes
3
replies
248
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated just now by
Ram
43k • written 13 days ago by
Adyasha
• 0
0
votes
1
reply
248
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Sony
▴ 10
0
votes
1
reply
244
views
merging Seurat objects after SCT
Seurat
SCT
updated 28 days ago by
Ram
43k • written 28 days ago by
michelle.swarovski
• 0
0
votes
1
reply
243
views
Subsetting and merging back Seurat Object brings different results
Seurat
11 days ago by
Bine
▴ 60
0
votes
2
replies
242
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
6 days ago by
Ahiad Chen Zion
• 0
1
vote
3
replies
238
views
STAR aligner error
RNA-seq
STAR
slurm
updated 5 days ago by
Ram
43k • written 6 days ago by
M.
▴ 30
0
votes
3
replies
237
views
Software to separate reads from different individuals
software
development
nanopore
updated 14 days ago by
GenoMax
142k • written 14 days ago by
njornet
▴ 20
1
vote
2
replies
236
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 13 days ago by
Ram
43k • written 13 days ago by
Ravita
• 0
1
vote
3
replies
235
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 4 days ago by
GenoMax
142k • written 4 days ago by
cput
• 0
390 results • Page
4 of 8
Recent Votes
Best way to query VCF for specific variants
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
A: Is Bam One-Based Or Zero-Based?
A: Is Bam One-Based Or Zero-Based?
A: Data Set Suitable For Comparing Wgs, Exome, And Rna-Seq Data Generated From The
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
Practical Haplotype Graph v2 not finding correct paths
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Recent Replies
Comment: How to process Bulk WES data?
by
GenoMax
142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinve: https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
GenoMax
142k
You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t
by
mropri
▴ 150
Hi swbarnes2, that was the problem, they were not numeric but as character columns. converted them and it fixed the error. Thank you for yo…
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Prawesh
• 0
I figured out: Since featureCounts counts fragments and not reads, we have pair-end data that means **Assigned** value from the output w…
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
> My question is this: "mate reverse strand" (flag 16/0x10) or "read reverse strand" (flag 32/0x20) do not directly relate to the strandedn…
Answer: How to interpret infinite odds ratio?
by
bhumm
▴ 140
As you stated, your problem is likely division by 0. See this [Cross-Validated][1] post that seems to be very similar to your problem. In …
Comment: Duplicated sequence samtools
by
GenoMax
142k
Consider using SLURM job arrays if you want to use a `for` loop inside a single SLURM job: https://hpc.nmsu.edu/discovery/slurm/job-arrays/
Answer: Duplicated sequence samtools
by
Pierre Lindenbaum
161k
the sequence c_000007023807_aloha2_low_cov is duplicated in the reference grep c_000007023807_aloha2_low_cov path/to/reference.fasta
Comment: imputation through beagle
by
analyst
▴ 50
Thank you so much dthorbur. Yes I am new to imputation analysis. I will follow your kind suggestions. Thanks again!
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lagartija
▴ 160
I don't know but another way of doing it would be to combine different datasets of different strains that you know are clonal. Then you kno…
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★ 2.4k
Please check out these posts https://www.biostars.org/p/367626/
Comment: Galaxy StringTie error
by
trkfs
• 0
will do, thank you
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by
bk11
★ 2.4k
You can do the following- ```r Idents(SeuratObj) <- "orig.ident" control_set <- subset(SeuratObj, idents = c("counts.control","data.contro…
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