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1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.1 years ago by
midox
▴ 290
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.4 years ago by
Leite
★ 1.3k
24
votes
25
replies
8.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.7 years ago by
dpc
▴ 240
23
votes
22
replies
49k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 17 months ago by
Nicole
• 0 • written 6.0 years ago by
gaelgarcia
▴ 260
23
votes
10
replies
5.8k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 3.0 years ago by
Kevin Blighe
87k • written 6.2 years ago by
Joe
▴ 40
22
votes
19
replies
3.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.5 years ago by
zizigolu
★ 4.3k
22
votes
20
replies
2.5k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 12 months ago by
Ram
43k • written 7.8 years ago by
Farbod
★ 3.4k
20
votes
17
replies
6.0k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.7 years ago by
Anand Rao
▴ 630
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 21 months ago by
Ram
43k • written 8.3 years ago by
dam4l
▴ 200
20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by
1769mkc
★ 1.2k • written 3.2 years ago by
pomodoro_sinensis
▴ 110
19
votes
43
replies
5.6k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by
nazaninhoseinkhan
▴ 520
18
votes
7
replies
1.4k
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
19 months ago by
Rafael Soler
★ 1.2k
18
votes
4
replies
8.7k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 14 months ago by
Ram
43k • written 10.7 years ago by
user
▴ 940
18
votes
19
replies
2.3k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 17 months ago by
Ram
43k • written 5.3 years ago by
rbkh09
• 0
17
votes
8
replies
2.3k
views
Number of unique authors in PubMed in last 10 years
PubMed
8.1 years ago by
nejc
▴ 50
17
votes
13
replies
6.5k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
6.9 years ago by
lghust2011
▴ 110
17
votes
19
replies
2.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.7 years ago by
Gian77
▴ 60
17
votes
37
replies
4.7k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.9 years ago by
Biostar
20 • written 5.0 years ago by
williamsbrian5064
▴ 510
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
16
votes
16
replies
3.1k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
6.1 years ago by
bioinfo456
▴ 150
16
votes
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.8 years ago by
salamandra
▴ 550
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.5 years ago by
dimitrischat
▴ 210
16
votes
10
replies
5.6k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
7.9 years ago by
Alternative
▴ 270
16
votes
18
replies
5.5k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.7 years ago by
Mensur Dlakic
★ 27k • written 4.7 years ago by
tikshyadav19
• 0
16
votes
21
replies
2.2k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.6 years ago by
Farbod
★ 3.4k
15
votes
14
replies
3.2k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
6.3 years ago by
John
▴ 270
15
votes
19
replies
1.9k
views
trimmomaric command for a fasta file?
trimmomatic
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
Nadin.asal
• 0
15
votes
11
replies
7.2k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
5.5 years ago by
jackgrayner
▴ 100
15
votes
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by
GenoMax
141k • written 7 months ago by
1769mkc
★ 1.2k
15
votes
14
replies
1.9k
views
how can interpret these biologically weird results?
RNA-Seq
updated 3.3 years ago by
Biostar
20 • written 6.5 years ago by
Mozart
▴ 330
14
votes
8
replies
5.0k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
10.5 years ago by
Dan D
7.4k
14
votes
10
replies
910
views
How to remove center population from seurat cluster
single-cell
4 months ago by
synat.keam
▴ 100
14
votes
5
replies
3.1k
views
bioinformatics basic training
genome
updated 13 months ago by
Ram
43k • written 9.4 years ago by
f.muoghalu
• 0
14
votes
18
replies
2.2k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 200 • written 7 months ago by
Chris
▴ 260
14
votes
18
replies
4.9k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 7.3 years ago by
Biostar
20 • written 7.5 years ago by
plink_9857
▴ 50
14
votes
30
replies
3.4k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
5.0 years ago by
Malka
▴ 80
14
votes
16
replies
1.9k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 3.5 years ago by
lieven.sterck
15k • written 3.5 years ago by
utsafar
▴ 80
13
votes
7
replies
6.6k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 7.4 years ago by
Biostar
20 • written 7.4 years ago by
Raheleh
▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 8 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
13
votes
13
replies
1.5k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
4.5 years ago by
DanielC
▴ 170
13
votes
13
replies
9.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 6.1 years ago by
Devon Ryan
104k • written 6.1 years ago by
amitgourav.ghosh12
▴ 70
13
votes
16
replies
7.2k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
5.3 years ago by
DNAngel
▴ 250
13
votes
16
replies
6.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
7.3 years ago by
Paul
★ 1.5k
13
votes
6
replies
4.0k
views
bcftools isec -n operators
bcftools
intersect
updated 2.7 years ago by
Ram
43k • written 4.3 years ago by
Begonia_pavonina
▴ 150
13
votes
4
replies
23k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
7.0 years ago by
ariel.balter
▴ 260
13
votes
13
replies
17k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.7 years ago by
Arindam Ghosh
▴ 510
13
votes
24
replies
4.6k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 7.1 years ago by
GenoMax
141k • written 7.1 years ago by
Gary
▴ 480
13
votes
19
replies
5.4k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.4 years ago by
bioplanet
▴ 60
12
votes
10
replies
4.1k
views
Speed up BLASTp vs NCBI nr database
blast
7.9 years ago by
biotech
▴ 570
12
votes
28
replies
2.7k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.9 years ago by
Za
▴ 140
1,000 results • Page
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Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
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Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
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In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
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by
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141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
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I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
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82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
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by
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161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold
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ginellegrenier
• 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
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jkim
▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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by
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Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
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• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
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by
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141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
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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 …
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