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109 results • Page 1 of 3
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0
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12
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Calling SE and TE using ROSE
Calling SE
33 minutes ago by Manhezz • 0
0
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0
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20
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BLAST using both nucleotides and taxonomic local databases
blast ncbi taxid taxonomy
1 hour ago by Begonia_pavonina ▴ 150
0
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1
reply
38
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Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
updated 1 hour ago by 161k • written 2 hours ago by • 0
0
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0
replies
33
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
3 hours ago by Aspire ▴ 300
0
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2
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96
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Highest variable features in single cell data
cell single
2 hours ago by Kazo • 0
0
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0
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64
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PCA plot
DESeq2 PCAplot
9 hours ago by Aaliya ▴ 10
0
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0
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68
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Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
11 hours ago by 4fzcgueyp5 • 0
0
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1
reply
124
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Annovar using R package
Annovar gnomAD R
updated 14 hours ago by 161k • written 16 hours ago by ▴ 40
0
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5
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208
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Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 21 hours ago by 141k • written 22 hours ago by ▴ 90
0
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0
replies
94
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 17 hours ago by 43k • written 22 hours ago by • 0
0
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0
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156
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
22 hours ago by pramach1 ▴ 40
0
votes
1
reply
111
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 21 hours ago by • 0 • written 1 day ago by • 0
0
votes
0
replies
98
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
1 day ago by salias • 0
0
votes
4
replies
201
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
4 hours ago by sehriban.buyukkilic ▴ 10
0
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0
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86
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 17 hours ago by 43k • written 1 day ago by • 0
1
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2
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161
views
alignment result
RNA-seq samtools hisat2
6 hours ago by ahmad.sajad4541 • 0
0
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0
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77
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet DoubletFinder Seurat modelHomotypic
updated 17 hours ago by 43k • written 1 day ago by • 0
0
votes
0
replies
89
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
1 day ago by Kash ▴ 110
0
votes
1
reply
127
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 1 day ago by ★ 27k • written 1 day ago by • 0
0
votes
2
replies
216
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 17 hours ago by 43k • written 1 day ago by ▴ 140
2
votes
9
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807
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 1 day ago by 4.2k • written 6 months ago by • 0
0
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10
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378
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
1 day ago by atowns21 • 0
0
votes
1
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142
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 1 day ago by ★ 2.3k • written 1 day ago by • 0
0
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0
replies
89
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The concept of co-occurrence network structure
co-occurence microbiome network
1 day ago by ohtang7 ▴ 40
0
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1
reply
144
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Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 1 day ago by 141k • written 1 day ago by ▴ 20
0
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5
replies
276
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
1 day ago by njornet ▴ 20
0
votes
0
replies
82
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 1 day ago by 43k • written 2 days ago by • 0
0
votes
0
replies
90
views
Merging replicates from Encode project
CHIP-seq encode
2 days ago by Nurken • 0
1
vote
3
replies
193
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
2 days ago by WouterDeCoster 47k
1
vote
3
replies
229
views
some error in building kraken2 database
metagenome kraken2
1 day ago by Art1ess • 0
0
votes
1
reply
123
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 1 day ago by ★ 2.3k • written 2 days ago by ▴ 110
1
vote
1
reply
157
views
Failed kmer content
kmer illumina ngs
updated 1 day ago by 43k • written 2 days ago by • 0
0
votes
0
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80
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 1 day ago by 43k • written 2 days ago by • 0
0
votes
1
reply
134
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 2 days ago by 43k • written 2 days ago by • 0
0
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8
replies
283
views
Error in cnetplot enrichplot package
R
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
0
replies
103
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 2 days ago by 43k • written 2 days ago by ▴ 200
0
votes
0
replies
86
views
Analysis of the gene family of a genome.
Genome gene-family
updated 2 days ago by 43k • written 2 days ago by ▴ 80
0
votes
0
replies
90
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 1 day ago by 43k • written 2 days ago by • 0
0
votes
0
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164
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 2 days ago by 43k • written 2 days ago by ▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 2 days ago by 10k • written 6.1 years ago by ▴ 10
1
vote
5
replies
247
views
Downsampling fastq file
downsample fastq
updated 2 days ago by 43k • written 2 days ago by ▴ 80
0
votes
1
reply
122
views
tbtool
tbtool
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
2
replies
180
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 2 days ago by 19k • written 2 days ago by • 0
0
votes
1
reply
115
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 2 days ago by 82k • written 2 days ago by • 0
0
votes
0
replies
81
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
2 days ago by manaswwm ▴ 490
0
votes
0
replies
73
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by alifafiq1 • 0
0
votes
0
replies
78
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
3 days ago by feather-W • 0
2
votes
4
replies
243
views
interpretartion of a vcf file
calling genotype ONT variant diploid
1 day ago by samuelkalandarov2002 ▴ 10
0
votes
0
replies
77
views
Annotating single cell data automatically
cell annotation single
3 days ago by Gerard • 0
0
votes
1
reply
140
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by 141k • written 3 days ago by • 0
109 results • Page 1 of 3
Recent Votes
discoSnp - reference-free finding of isolated SNPs from non assembled reads
Comment: Figures are disappeared from html report of SnpEff
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
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Recent Awards • All
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Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
At this point you should email NCBI help desk and ask them this question. If you get an answer then please post it back in this thread.
Comment: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data by Kazo • 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work? by Assa Yeroslaviz ★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error by Adrian Altenhoff ★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid by ashaneev07 ▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM by dsull ★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file by Pierre Lindenbaum 161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file by Maria • 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
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