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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
14
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
14 minutes ago by
Dylan
• 0
0
votes
1
reply
11
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 6 minutes ago by
GenoMax
141k • written 24 minutes ago by
Lada
▴ 30
0
votes
0
replies
13
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 hour ago by
ohtang7
▴ 40
0
votes
0
replies
18
views
How to merge UMAP coordinates with the concatenated loom files in anndata object
RNA-velocity
scanpy
loomfile
scvelo
python
1 hour ago by
Kash
▴ 110
0
votes
1
reply
65
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 4 hours ago by
GenoMax
141k • written 4 hours ago by
Srinka
▴ 20
0
votes
4
replies
124
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 2 hours ago by
GenoMax
141k • written 4 hours ago by
njornet
▴ 20
0
votes
0
replies
34
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 hours ago by
Ram
43k • written 5 hours ago by
SHREYA
• 0
0
votes
0
replies
39
views
Merging replicates from Encode project
CHIP-seq
encode
5 hours ago by
Nurken
• 0
1
vote
3
replies
135
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
6 hours ago by
WouterDeCoster
47k
0
votes
2
replies
106
views
some error in building kraken2 database
metagenome
kraken2
updated 2 hours ago by
Ram
43k • written 7 hours ago by
Art1ess
• 0
0
votes
1
reply
57
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 hours ago by
bk11
★ 2.3k • written 8 hours ago by
Susmita Mandal
▴ 110
1
vote
1
reply
105
views
Failed kmer content
kmer
illumina
ngs
updated 2 hours ago by
Ram
43k • written 10 hours ago by
Kasturi
• 0
0
votes
1
reply
101
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 9 hours ago by
Basti
★ 2.0k • written 11 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
58
views
Seurat merge and batch correction
Seurat
13 hours ago by
sooni
▴ 20
0
votes
0
replies
44
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 1 hour ago by
Ram
43k • written 13 hours ago by
SSSJec
• 0
0
votes
1
reply
101
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 21 hours ago by
Ram
43k • written 21 hours ago by
Cameron.walker9900
• 0
0
votes
8
replies
233
views
Error in cnetplot enrichplot package
R
updated 20 hours ago by
Ram
43k • written 22 hours ago by
Farhad
• 0
0
votes
0
replies
76
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 22 hours ago by
Ram
43k • written 22 hours ago by
maxime.policarpo
▴ 200
0
votes
0
replies
63
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 22 hours ago by
Ram
43k • written 22 hours ago by
sansan_96
▴ 80
0
votes
2
replies
121
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
20 hours ago by
dxj294
• 0
0
votes
0
replies
68
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 hours ago by
Ram
43k • written 22 hours ago by
Amélie
• 0
0
votes
0
replies
103
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 22 hours ago by
Ram
43k • written 23 hours ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 20 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
0
replies
71
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Abeer
• 0
0
votes
1
reply
111
views
tbtool
tbtool
updated 1 day ago by
Ram
43k • written 1 day ago by
Raman
• 0
0
votes
2
replies
163
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 23 hours ago by
i.sudbery
19k • written 1 day ago by
Patadu94
• 0
0
votes
2
replies
136
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
emmanouil.a
▴ 120
0
votes
1
reply
106
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 1 day ago by
ATpoint
81k • written 1 day ago by
enanoide
• 0
0
votes
0
replies
76
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
1 day ago by
manaswwm
▴ 490
0
votes
0
replies
66
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
6 hours ago by
alifafiq1
• 0
0
votes
0
replies
75
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
1 day ago by
feather-W
• 0
2
votes
3
replies
175
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated 7 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
70
views
Annotating single cell data automatically
cell
annotation
single
1 day ago by
Gerard
• 0
0
votes
1
reply
129
views
RNA-seq bacteria contamination
RNA-seq
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sh
• 0
0
votes
0
replies
64
views
Imputation advice
imputation
1 day ago by
kl
▴ 10
0
votes
0
replies
80
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
1 day ago by
Enrique
• 0
0
votes
0
replies
67
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
1 day ago by
sativus
▴ 20
0
votes
0
replies
69
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
1 day ago by
Biostars2200
• 0
0
votes
0
replies
104
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 1 day ago by
Carlo Yague
8.7k • written 1 day ago by
Atul K.
• 0
1
vote
5
replies
401
views
Marking duplicates using UMIs
Deduplication
UMI
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Lipika
• 0
0
votes
0
replies
132
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 2 days ago by
Ram
43k • written 2 days ago by
sainavyav22
• 0
0
votes
0
replies
133
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
2 days ago by
rthapa
▴ 90
0
votes
0
replies
124
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
2 days ago by
Mamatha Y S
• 0
0
votes
2
replies
242
views
bam merging for archaic samples
samtools
bam
updated 2 days ago by
Ram
43k • written 3 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
524
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
3 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
202
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
3 days ago by
abhishekghadge
• 0
2
votes
5
replies
660
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 2 days ago by
Jesse
▴ 740 • written 3 days ago by
Ann
★ 2.4k
0
votes
0
replies
180
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 3 days ago by
Ram
43k • written 3 days ago by
mja
• 0
0
votes
0
replies
183
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
3 days ago by
Nitin
• 0
0
votes
0
replies
183
views
absolute path for symbolic links in Snakefile
Snakemake
updated 3 days ago by
Ram
43k • written 4 days ago by
yifangt86
▴ 60
1,000 results • Page
1 of 20
Recent Votes
Comment: How to convert plink files to Hapmap Format
Am I crazy, or are most published RNA-seq studies vastly underpowered?
Trimming sequences based on NCBI contamination screen report
warning[vg::giraffe]: Cannot cluster reads with a fragment distance smaller than read distance
Answer: Redirection of Duplicate PMIDs
Answer: How to convert plink files to Hapmap Format
Answer: How to convert plink files to Hapmap Format
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Recent Awards •
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Great Question
to
Ann
★ 2.4k
Scholar
to
marco.barr
▴ 80
Popular Question
to
Kash
▴ 110
Scholar
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GenoMax
141k
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anovak
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pfee418
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sarahmanderni
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Recent Replies
Comment: Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Ser
by
atowns21
• 0
@benjamin.pyenson and @Ram could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or d…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts. If you had extraneous sequence…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please answer my above question. What type of data is it, binary (cases and controls) or quantitative? You need to update Phenotype info in…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
This is how my .fam file looks like ![enter image description here][1] [1]: /media/images/caccd97c-3606-48d2-aa32-423a9882 And I run …
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
> linked to a list of grants Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this w…
Answer: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Hi Dominick, One thing I am not sure of is, how is it that you got the other PMID in the first place? The reason I ask is that you mentio…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thanks Marco, btw do you have any idea why I get this "Warning: Skipping --assoc/--model since less than two phenotypes are present." aft…
Comment: Subset Seurat object from Xenium spatial data
by
bk11
★ 2.3k
For subsetting a sample, you can do something like this- Idents(seuratObj) <- "orig.ident" subj1 <- c("subject_1") subj1_seur…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Ok! I have a recommendation. I'll submit it as an answer, pending your feedback. vincent
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
In modeller we need to use templates as well.so 63% is acceptable
Comment: DYH17 Structure Prediction
by
Ram
43k
Mensur said > The latter option assumes you know how to use Modeller Do you know how to use Modeller? I vaguely recall there being a mini…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
ATpoint
81k
I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
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