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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
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
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
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
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
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
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
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
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
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 3.2 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
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
10
replies
905
views
How to remove center population from seurat cluster
single-cell
4 months ago by
synat.keam
▴ 100
14
votes
18
replies
2.2k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 200 • written 6 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
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
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
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
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 7 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
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
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
▴ 80
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
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
19
replies
5.4k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.4 years ago by
bioplanet
▴ 60
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
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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Recent Votes
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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A: Where To Download Pam50 Gene Set?
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Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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