Limit : all time
all time today this week this month this year
1,000 results • Page 5 of 20
Sort: Rank
Rank Views Votes Replies
0
votes
5
replies
437
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 20 days ago by 142k • written 21 days ago by ▴ 90
0
votes
0
replies
166
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 20 days ago by 43k • written 21 days ago by • 0
0
votes
0
replies
328
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
21 days ago by pramach1 ▴ 40
0
votes
1
reply
204
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 21 days ago by • 0 • written 21 days ago by • 0
0
votes
0
replies
167
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
21 days ago by salias • 0
0
votes
5
replies
455
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 18 days ago by 100k • written 21 days ago by ▴ 10
0
votes
0
replies
141
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 20 days ago by 43k • written 21 days ago by • 0
1
vote
2
replies
280
views
alignment result
RNA-seq samtools hisat2
20 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
139
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
21 days ago by Kash ▴ 110
0
votes
1
reply
188
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 21 days ago by ★ 27k • written 21 days ago by • 0
2
votes
2
replies
333
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 20 days ago by 43k • written 21 days ago by ▴ 140
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 21 days ago by 4.2k • written 7 months ago by • 0
0
votes
11
replies
704
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
19 days ago by atowns21 • 0
0
votes
1
reply
211
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 21 days ago by ★ 2.4k • written 21 days ago by • 0
0
votes
0
replies
119
views
The concept of co-occurrence network structure
co-occurence microbiome network
22 days ago by ohtang7 ▴ 40
0
votes
1
reply
205
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 22 days ago by 142k • written 22 days ago by ▴ 20
0
votes
5
replies
423
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
21 days ago by njornet ▴ 20
0
votes
0
replies
124
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 22 days ago by 43k • written 22 days ago by • 0
0
votes
0
replies
126
views
Merging replicates from Encode project
CHIP-seq encode
22 days ago by Nurken • 0
1
vote
3
replies
299
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
22 days ago by WouterDeCoster 47k
1
vote
3
replies
333
views
some error in building kraken2 database
metagenome kraken2
21 days ago by Art1ess • 0
0
votes
1
reply
209
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 22 days ago by ★ 2.4k • written 22 days ago by ▴ 110
1
vote
1
reply
210
views
Failed kmer content
kmer illumina ngs
updated 22 days ago by 43k • written 22 days ago by • 0
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 22 days ago by 43k • written 22 days ago by • 0
0
votes
1
reply
174
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 22 days ago by 43k • written 22 days ago by • 0
0
votes
8
replies
453
views
Error in cnetplot enrichplot package
R
updated 22 days ago by 43k • written 22 days ago by • 0
0
votes
0
replies
128
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 22 days ago by 43k • written 22 days ago by ▴ 200
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome gene-family
updated 22 days ago by 43k • written 22 days ago by ▴ 90
0
votes
0
replies
115
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 22 days ago by 43k • written 22 days ago by • 0
0
votes
0
replies
222
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 22 days ago by 43k • written 22 days ago by ▴ 20
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 22 days ago by 10k • written 6.2 years ago by ▴ 10
1
vote
8
replies
531
views
Downsampling fastq file
downsample fastq
14 days ago by marco.barr ▴ 110
0
votes
1
reply
168
views
tbtool
tbtool
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
10
replies
605
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 15 days ago by 19k • written 23 days ago by • 0
0
votes
1
reply
158
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 23 days ago by 82k • written 23 days ago by • 0
0
votes
0
replies
105
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
23 days ago by manaswwm ▴ 510
0
votes
0
replies
96
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
22 days ago by alifafiq1 • 0
0
votes
0
replies
102
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
23 days ago by feather-W • 0
2
votes
4
replies
375
views
interpretartion of a vcf file
calling genotype ONT variant diploid
21 days ago by samuelkalandarov2002 ▴ 10
0
votes
0
replies
98
views
Annotating single cell data automatically
cell annotation single
23 days ago by Gerard • 0
0
votes
1
reply
198
views
RNA-seq bacteria contamination
RNA-seq
updated 23 days ago by 142k • written 23 days ago by • 0
0
votes
0
replies
95
views
Imputation advice
imputation
23 days ago by kl ▴ 10
0
votes
0
replies
117
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
23 days ago by Enrique • 0
0
votes
0
replies
91
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
23 days ago by sativus ▴ 20
0
votes
0
replies
96
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
23 days ago by Biostars2200 • 0
0
votes
0
replies
155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 23 days ago by 8.7k • written 23 days ago by • 0
2
votes
5
replies
528
views
Marking duplicates using UMIs
Deduplication UMI
updated 23 days ago by 19k • written 24 days ago by • 0
0
votes
0
replies
156
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 24 days ago by 43k • written 24 days ago by • 0
0
votes
0
replies
161
views
Bacterial genome alignment with mauve
Bacteria mauve genome
24 days ago by rthapa ▴ 90
0
votes
0
replies
155
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
24 days ago by Mamatha Y S • 0
1,000 results • Page 5 of 20
Recent Votes
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: genome finishing
Recent Locations • All
Cambridge, MA, 2 minutes ago
Germany, 4 minutes ago
Belgium, 4 minutes ago
France, 4 minutes ago
United States, 5 minutes ago
United States, 6 minutes ago
Sheffield, UK, 6 minutes ago
Recent Awards • All
Scholar to rpolicastro 13k
Popular Question to Amr ▴ 160
Popular Question to asalimih ▴ 60
Popular Question to nd48 ▴ 20
Scholar to Trivas ★ 1.8k
Popular Question to biology_inform ▴ 50
Popular Question to Joe 21k
Recent Replies
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file by asalimih ▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R by Lélé • 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations by GenoMax 142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations by Pierre Lindenbaum 161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R by Ghada • 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R by jared.andrews07 ★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing by GenoMax 142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda by Pierre Lindenbaum 161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: Cannot install bwa-mem2 via conda by Istvan Albert 100k
The problem is caused by running the ARM-based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that versio…
Comment: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
[https://www.biostars.org/p/9559284/][1] you could try this [1]: https://www.biostars.org/p/9559284/
Comment: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
it's also true that now I only have one pod5 folder, thanks anyway for clarifying the focus of the issue. Yes, they are probably secondary …
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
I'm unsure. I will say that looking for [ normalize](https://github.com/search?q=repo%3Atanaylab%2Fmetacells%20normalize&type=code) among t…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data by Pierre Lindenbaum 161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: genome finishing by nd48 ▴ 20
What is the input? Do you have short reads (e.g. illumina 100bp paired reads)? As mentioned already, you already have the consensus i.e. c…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data by biology_inform ▴ 50
I've been exploring different visualization tools like Circos and shinyCircos, and I've noticed that they require an input file similar to …
Traffic: 2895 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6