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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
3.8 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
20
replies
2.6k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 13 months ago by
Ram
43k • written 7.8 years ago by
Farbod
★ 3.4k
22
votes
19
replies
3.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.6 years ago by
zizigolu
★ 4.3k
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
17
replies
3.3k
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
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
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
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
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
17
votes
13
replies
6.6k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
7.0 years ago by
lghust2011
▴ 110
17
votes
8
replies
2.4k
views
Number of unique authors in PubMed in last 10 years
PubMed
8.1 years ago by
nejc
▴ 50
17
votes
37
replies
4.8k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.9 years ago by
Biostar
20 • written 5.1 years ago by
williamsbrian5064
▴ 510
17
votes
19
replies
2.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.7 years ago by
Gian77
▴ 60
16
votes
21
replies
2.3k
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
16
votes
16
replies
3.2k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
6.1 years ago by
bioinfo456
▴ 150
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.5 years ago by
dimitrischat
▴ 210
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
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.9 years ago by
salamandra
▴ 550
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
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
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
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
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
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by
GenoMax
142k • 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
10.6 years ago by
Dan D
7.4k
14
votes
5
replies
3.2k
views
bioinformatics basic training
genome
updated 13 months ago by
Ram
43k • written 9.4 years ago by
f.muoghalu
• 0
14
votes
16
replies
2.0k
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
14
votes
10
replies
944
views
How to remove center population from seurat cluster
single-cell
4 months ago by
synat.keam
▴ 100
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
18
replies
2.3k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 200 • written 7 months ago by
Chris
▴ 260
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 7.5 years ago by
Raheleh
▴ 260
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
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 15 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
13
votes
13
replies
18k
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
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
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
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
142k • written 7.1 years ago by
Gary
▴ 480
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
13
replies
9.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 6.2 years ago by
Devon Ryan
104k • written 6.2 years ago by
amitgourav.ghosh12
▴ 70
13
votes
19
replies
5.4k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.4 years ago by
bioplanet
▴ 60
12
votes
13
replies
2.8k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 17 months ago by
Ram
43k • written 8.8 years ago by
sarathkurichiyil
• 0
12
votes
8
replies
3.2k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
7.3 years ago by
statfa
▴ 760
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Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Define enhancer regions
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Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Discrepancy in read counts from fastq
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Comment: Discrepancy in read counts from fastq
by
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82k
Honestly, you're using two different approaches and it is unclear whether they're doing the exact same math under the hood in terms of call…
Answer: Subsetting and merging back Seurat Object brings different results
by
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Noone has an idea? Thank you!
Answer: Bacterial plasmid analysis
by
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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…
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by
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82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
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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…
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★ 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…
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by
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If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
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by
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Thank you so much. I'm new to this and didn't realise there was a code option.
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Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
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Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
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142k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
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82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
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