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184 results • Page
4 of 4
Sort: Rank
Rank
Views
Votes
Replies
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
5 days ago by
Azra
▴ 10
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
0
votes
2
replies
235
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
5 days ago by
analyst
▴ 50
0
votes
6
replies
427
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
548
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
6 days ago by
Tuck898
• 0
2
votes
9
replies
708
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 11 days ago by
schmince
• 0
0
votes
5
replies
323
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
5 days ago by
SilhouetteQ
• 0
0
votes
5
replies
337
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
5 days ago by
feather-W
• 0
1
vote
4
replies
344
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 5 days ago by
Ram
43k • written 10 days ago by
samRayne
• 0
1
vote
4
replies
307
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 13 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
0
votes
2
replies
233
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 10 days ago by
elisheva
▴ 120
5
votes
7
replies
500
views
RNA seq analysis
DESeq
RNA-seq
3 days ago by
Jacek
▴ 20
0
votes
9
replies
612
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 3 days ago by
Wayne
★ 2.0k • written 12 days ago by
JACKY
▴ 140
0
votes
1
reply
149
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 5 days ago by
Ram
43k • written 12 days ago by
David
• 0
1
vote
1
reply
185
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Jordan M Eizenga
▴ 460 • written 12 days ago by
sarumonsus
▴ 10
0
votes
3
replies
361
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
5 days ago by
mropri
▴ 150
3
votes
6
replies
504
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 6 days ago by
Pine
▴ 20 • written 13 days ago by
snajafy
• 0
0
votes
2
replies
307
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
4
votes
7
replies
427
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
5 days ago by
Chen
• 0
3
votes
3
replies
274
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 5 days ago by
Ram
43k • written 18 days ago by
Adyasha
• 0
0
votes
7
replies
447
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 5 days ago by
Mohamed Abderrahmane
▴ 20 • written 19 days ago by
matteo.levorato
• 0
0
votes
0
replies
124
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 5 days ago by
Ram
43k • written 19 days ago by
atharvakarkare14
▴ 40
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
4 days ago by
Emily
▴ 20
2
votes
3
replies
280
views
Finding variants within a subset of a BAM file
variant
calling
4 days ago by
ramiro.barrantes
• 0
0
votes
2
replies
280
views
Traveler with Infernal mapping failed
r2dt
updated 2 hours ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
9
replies
603
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
3 days ago by
Arton
▴ 10
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
3 days ago by
Arton
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 5 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
3
replies
800
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 2 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 20 hours ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 5 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 5 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 1 day ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 6 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
184 results • Page
4 of 4
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Recent Replies
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
by
anton.i.petrov
• 0
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
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
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…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
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 …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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