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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
3
replies
250
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
9 days ago by
WouterDeCoster
47k
1
vote
3
replies
284
views
some error in building kraken2 database
metagenome
kraken2
8 days ago by
Art1ess
• 0
0
votes
1
reply
161
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 8 days ago by
bk11
★ 2.4k • written 9 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
184
views
Failed kmer content
kmer
illumina
ngs
updated 8 days ago by
Ram
43k • written 9 days ago by
Kasturi
• 0
0
votes
0
replies
96
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 8 days ago by
Ram
43k • written 9 days ago by
SSSJec
• 0
0
votes
1
reply
153
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 9 days ago by
Ram
43k • written 9 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
363
views
Error in cnetplot enrichplot package
R
updated 9 days ago by
Ram
43k • written 9 days ago by
Farhad
• 0
0
votes
0
replies
113
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 9 days ago by
Ram
43k • written 9 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
98
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 9 days ago by
Ram
43k • written 9 days ago by
sansan_96
▴ 80
0
votes
0
replies
104
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 8 days ago by
Ram
43k • written 9 days ago by
Amélie
• 0
0
votes
0
replies
206
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 9 days ago by
Ram
43k • written 9 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 9 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
8
replies
435
views
Downsampling fastq file
downsample
fastq
1 day ago by
marco.barr
▴ 90
0
votes
1
reply
144
views
tbtool
tbtool
updated 9 days ago by
Ram
43k • written 9 days ago by
Raman
• 0
0
votes
10
replies
479
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 9 days ago by
Patadu94
• 0
0
votes
1
reply
137
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 10 days ago by
ATpoint
82k • written 10 days ago by
enanoide
• 0
0
votes
0
replies
92
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
10 days ago by
manaswwm
▴ 510
0
votes
0
replies
82
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
9 days ago by
alifafiq1
• 0
0
votes
0
replies
88
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
10 days ago by
feather-W
• 0
2
votes
4
replies
310
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
8 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
89
views
Annotating single cell data automatically
cell
annotation
single
10 days ago by
Gerard
• 0
0
votes
1
reply
170
views
RNA-seq bacteria contamination
RNA-seq
updated 10 days ago by
GenoMax
142k • written 10 days ago by
sh
• 0
0
votes
0
replies
79
views
Imputation advice
imputation
10 days ago by
kl
▴ 10
0
votes
0
replies
98
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
10 days ago by
Enrique
• 0
0
votes
0
replies
79
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
10 days ago by
sativus
▴ 20
0
votes
0
replies
86
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
10 days ago by
Biostars2200
• 0
0
votes
0
replies
139
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 10 days ago by
Carlo Yague
8.7k • written 10 days ago by
Atul K.
• 0
2
votes
5
replies
478
views
Marking duplicates using UMIs
Deduplication
UMI
updated 10 days ago by
i.sudbery
19k • written 11 days ago by
Lipika
• 0
0
votes
0
replies
144
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 10 days ago by
Ram
43k • written 11 days ago by
sainavyav22
• 0
0
votes
0
replies
147
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
11 days ago by
rthapa
▴ 90
0
votes
0
replies
140
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
11 days ago by
Mamatha Y S
• 0
0
votes
2
replies
280
views
bam merging for archaic samples
samtools
bam
updated 10 days ago by
Ram
43k • written 12 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
545
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
12 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
226
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
11 days ago by
abhishekghadge
• 0
2
votes
5
replies
713
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 11 days ago by
Jesse
▴ 740 • written 12 days ago by
Ann
★ 2.4k
0
votes
0
replies
194
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 12 days ago by
Ram
43k • written 12 days ago by
mja
• 0
0
votes
0
replies
193
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
12 days ago by
Nitin
• 0
0
votes
0
replies
187
views
Chemical structure validation
structure
cap
validation
metabolite
12 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
275
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 12 days ago by
GenoMax
142k • written 12 days ago by
bioyas
▴ 10
0
votes
0
replies
211
views
Copy number variation plot
Copy-number-variation
genomics
updated 12 days ago by
Ram
43k • written 12 days ago by
Emmi
• 0
0
votes
0
replies
187
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
12 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
293
views
Could you please assist in identifying this cluster?
single-cell
updated 12 days ago by
Ram
43k • written 12 days ago by
Kazo
▴ 10
0
votes
0
replies
209
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 12 days ago by
Ram
43k • written 13 days ago by
Dinmukhamed
• 0
0
votes
0
replies
204
views
miRDeep2: How to get the read counts
mirdeep2
13 days ago by
Atul K.
• 0
0
votes
0
replies
209
views
Lncipedia GTF file error
Proteomics
updated 12 days ago by
Ram
43k • written 13 days ago by
atharvakarkare14
▴ 20
3
votes
3
replies
498
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 12 days ago by
swbarnes2
14k • written 13 days ago by
noodle
▴ 580
0
votes
2
replies
566
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
13 days ago by
航太郎
• 0
0
votes
0
replies
224
views
create genewise sync file in popoolation
popoolation
updated 13 days ago by
GenoMax
142k • written 13 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
397
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
13 days ago by
Ashok
• 0
0
votes
2
replies
441
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
13 days ago by
Ashok
• 0
1,000 results • Page
3 of 20
Recent Votes
A: What is the difference between GRCh37 and hs37? And hg19?
A: Decoy In Reference Assembly
A: Decoy In Reference Assembly
Decoy In Reference Assembly
Decoy In Reference Assembly
Comment: Bacterial plasmid analysis
Unsupervised clustering on gene expression data
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massa.kassa.sc3na
▴ 600
Teacher
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Recent Replies
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
GenoMax
142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
Begonia_pavonina
▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq
by
GenoMax
142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
Comment: Bacterial plasmid analysis
by
Daria
▴ 10
I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Ok I think I know what happened. The order of cells changed, otherwise its the same: ![image](https://github.com/satijalab/seurat/assets/7…
Answer: Bacterial plasmid analysis
by
shenwei356
8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
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