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338 results • Page
2 of 7
Sort: Votes
Rank
Views
Votes
Replies
1
vote
3
replies
347
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 5 days ago by
GenoMax
136k • written 5 days ago by
bkffadia
• 0
1
vote
9
replies
343
views
Htseq-count reads with missing mate encountered
htseq
htseq-count
23 days ago by
Bjorn
• 0
1
vote
4
replies
387
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
21 days ago by
George
• 0
1
vote
2
replies
330
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 21 days ago by
Hongjin
• 0 • written 9 weeks ago by
mateomejias
• 0
1
vote
1
reply
242
views
Eigen_phred_coding values interpretation
variation
SNP
annotation
17 days ago by
Lukas
▴ 40
1
vote
1
reply
183
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 10 days ago by
CTLong
▴ 50 • written 12 days ago by
e.iich
• 0
1
vote
2
replies
294
views
A question about the missing or not observed alleles in PLINK datasets
PLINK
21 days ago by
abedkurdi10
▴ 190
1
vote
4
replies
298
views
Bowtie mapping for single_end read
bowtie
11 days ago by
Rita
• 0
1
vote
4
replies
428
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
22 days ago by
Daniel
▴ 30
1
vote
4
replies
317
views
Analyze with Geo2R
R
NCBI
15 days ago by
anasjamshed
▴ 120
1
vote
5
replies
343
views
bcftools mipileup error: format error, unexpected A at line 1
bcftools
updated 26 days ago by
Jautis
▴ 520 • written 26 days ago by
jiyoung
▴ 20
1
vote
3
replies
286
views
PMID multiple pdfs download using R
R
PubMed
updated 25 days ago by
Ram
41k • written 25 days ago by
Confused_human
▴ 20
1
vote
2
replies
189
views
recommend gene ranking methods when doing GSEA
Gene_rank
GSEA
1 day ago by
luckyday1661
• 0
1
vote
4
replies
242
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 3 days ago by
GenoMax
136k • written 4 days ago by
Javier
• 0
1
vote
4
replies
202
views
select unique samples in R
statistics
r
biostatistics
updated 2 days ago by
bk11
★ 1.8k • written 2 days ago by
Bioinfonext
▴ 440
1
vote
2
replies
246
views
ComBat-seq problem
ComBat-seq
RNA-Seq
batch-effect
updated 24 days ago by
Ram
41k • written 24 days ago by
Akash D
▴ 40
1
vote
5
replies
322
views
vcftools
vcftools
updated 5 days ago by
Barista
▴ 10 • written 5 days ago by
sevda
• 0
1
vote
1
reply
207
views
How to properly quantify gene expression of tandem duplicates from RNA-seq
pipeline
illumina
plants
RNA-seq
updated 26 days ago by
dthorbur
▴ 890 • written 26 days ago by
missTique
• 0
1
vote
5
replies
389
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 2 days ago by
Rory Stark
★ 2.0k • written 10 days ago by
DINESHR
• 0
1
vote
1
reply
210
views
Model matrix confront 2 groups out of 3
modelmatrix
r
designformula
deseq2
drimseq
updated 20 days ago by
ATpoint
78k • written 20 days ago by
dylannicoembros
• 0
1
vote
9
replies
626
views
Command line or python RNA-seq read simulator
simulation
RNA-seq
29 days ago by
i.sudbery
18k
1
vote
1
reply
184
views
RepeatModeler-2.0 BuildDatabase error
BuildDatabase
RepeatModeler
updated 24 days ago by
shelkmike
★ 1.1k • written 25 days ago by
1041853545
• 0
1
vote
2
replies
215
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 16 days ago by
WouterDeCoster
47k • written 16 days ago by
manaswiniparija3
▴ 10
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 17 days ago by
ayaosama2111
▴ 10 • written 7.1 years ago by
Nicolas Rosewick
10k
1
vote
6
replies
531
views
frequency plot for peaks
chip-seq
chipseeker
updated 10 days ago by
Ankit
▴ 400 • written 26 days ago by
Mehwish
▴ 10
1
vote
2
replies
254
views
Quality control on imputed genotypes for GWAS / application of PGS
qc
imputation
plink
regenie
gwas
25 days ago by
loy_loy
▴ 10
1
vote
1
reply
193
views
Match variants for allele frequency, LD score, and other features
snp
10 days ago by
Jautis
▴ 520
1
vote
2
replies
183
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease
Burden
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Shicheng Guo
★ 9.3k
1
vote
8
replies
534
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq
deseq2
19 days ago by
pingu77
▴ 20
1
vote
6
replies
549
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4
bwa-mem
target-capture-sequencing
alignment
16 days ago by
Miguel
• 0
1
vote
3
replies
337
views
gnomAD4.0 Hail Table Downloading
NGS
gnomAD
updated 22 days ago by
Ram
41k • written 22 days ago by
adarsh_pp
▴ 30
1
vote
0
replies
144
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
16 days ago by
WUSCHEL
▴ 720
1
vote
3
replies
287
views
Should unique gene names/transcript IDs be used for ribosomal gene copies in a GTF/GFF file?
GTF
GFF
updated 23 days ago by
dthorbur
▴ 890 • written 25 days ago by
cyril-cros
▴ 950
1
vote
7
replies
602
views
help with weird PCA? (vcfR)
vcftools
vcfR
R
28 days ago by
MaeBH
• 0
1
vote
8
replies
587
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM
RNA-Seq
mtDNA
23 days ago by
nick_b55
▴ 10
1
vote
1
reply
1.2k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 3 days ago by
charles.feigin
• 0 • written 7 weeks ago by
xinrantian
▴ 20
1
vote
5
replies
1.5k
views
BLAST: overflow error
BLAST
updated 5 days ago by
GenoMax
136k • written 19 months ago by
antoinefelden
▴ 60
1
vote
5
replies
230
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq
edgeR
DESeq2
RNA
ERCC
updated 1 day ago by
ATpoint
78k • written 1 day ago by
jips
• 0
1
vote
0
replies
247
views
Convert Seurat object to anndata
anndata
h5ad
Seurat
25 days ago by
nadammagdy
▴ 10
1
vote
0
replies
108
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
11 days ago by
joe
▴ 420
0
votes
3
replies
343
views
STAR GeneCounts for most genes are 0
STAR
RNA-seq
updated 26 days ago by
Ram
41k • written 26 days ago by
Hansel Ivander
• 0
0
votes
0
replies
109
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 10 days ago by
GenoMax
136k • written 10 days ago by
sativus
▴ 10
0
votes
3
replies
354
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 17 days ago by
MatthewP
★ 1.3k • written 18 days ago by
skinny_genes
• 0
0
votes
0
replies
43
views
Test for multiplicative effect in mendelian randomization?
R
mendelian_randomization
GWAS
7 hours ago by
clairvoyant
• 0
0
votes
1
reply
176
views
miRNA. Reads to long or to short
miRNA
updated 26 days ago by
biofalconch
★ 1.1k • written 26 days ago by
ju_ra
• 0
0
votes
0
replies
147
views
Outgroup for 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 2 days ago by
Ram
41k • written 4 months ago by
Morgan
• 0
0
votes
0
replies
117
views
NA values in conumee detail
cnv
copy-number
conumee
updated 18 days ago by
Ram
41k • written 19 days ago by
sativus
▴ 10
0
votes
1
reply
182
views
error uploading gct file to gsea
gsea
updated 24 days ago by
Barry Digby
★ 1.3k • written 27 days ago by
jabbari.parnian
▴ 30
0
votes
0
replies
206
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
promoter
motif
updated 5 days ago by
Ram
41k • written 8 days ago by
shome
▴ 10
0
votes
0
replies
101
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
2 days ago by
Agnia
• 0
338 results • Page
2 of 7
Recent Votes
Comment: GATK GetPileupSummaries Java heap space
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Recent Replies
Comment: which statistical test and which package for comapre datasets?
by
Jeremy
▴ 860
I think you will need at least three replicates to be able to do statistics.
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq
by
rpolicastro
12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq
by
RCMC
• 0
Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
how about using the bed file of your targets....
Answer: LCA from BLAST output
by
Dunois
★ 2.4k
You should probably be using `MMseqs2`'s `taxonomy` module for this: [https://github.com/soedinglab/MMseqs2#taxonomy][1] . [1]: https:/…
Comment: autodock vina on mac
by
iamsmor
• 0
thank you but ı am already follow this tutorial steps but at mgltools steps at the page but ı dont undertsand there isnot no enough explana…
Comment: How to create interval list from reference fasta or dict file?
by
Manuel Sokolov Ravasqueira
▴ 100
Hello @MatthewP , were you able to that for a fasta file for example? If you have a fasta file containing a targeted region, how to you ge…
Comment: WGCNA Dendrogram Branch missing from modules
by
andres.firrincieli
3.5k
I am not familiar with hdWGCNA but perhaps some modules are excluded because their genes are not expressed in a certain proportion of cells.
Comment: LCA from BLAST output
by
Michael
53k
If you know the lineage information is complete you could compare which columns are identical, however, there may be unranked levels in bet…
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Email the developers listed on contact page: https://chlorobox.mpimp-golm.mpg.de/contact.html
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136k
Curious as to what is `gentrome`? Genome decoy + transcriptome?
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