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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 4 months ago by
asalimih
▴ 60 • written 9.7 years ago by
mike
▴ 90
6
votes
25
replies
38k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 10 months ago by
13554221497
• 0 • written 6.1 years ago by
ARich
▴ 130
68
votes
25
replies
16k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 6 months ago by
GenoMax
141k • written 5.2 years ago by
Phil Ewels
★ 1.4k
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general
subjective
updated 6 months ago by
Ram
43k • written 14.3 years ago by
Giovanni M Dall'Olio
28k
17
votes
25
replies
2.4k
views
Tool:
Platform for Bioinformatics Students, Scholars and Scientists
sequence
genome
updated 10 months ago by
Ram
43k • written 8.2 years ago by
support
▴ 50
18
votes
25
replies
15k
views
13 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 9 months ago by
Pierre Lindenbaum
161k • written 2.3 years ago by
ConvolutedGenome
▴ 30
13
votes
25
replies
11k
views
9 follow
Tool:
Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis
sequencing
ngs
updated 10 months ago by
Ram
43k • written 10.7 years ago by
mikhail.shugay
3.5k
60
votes
25
replies
5.5k
views
8 follow
Forum:
Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size
statistical-power
RNA-Seq
updated 10 months ago by
Ram
43k • written 3.7 years ago by
telroyjatter
▴ 230
13
votes
25
replies
4.3k
views
7 follow
VEP output has no gene names
alignment
sequencing
vep
updated 10 months ago by
barslmn
★ 2.1k • written 5.7 years ago by
Gene_MMP8
▴ 240
38
votes
25
replies
9.1k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 7 months ago by
Ram
43k • written 8.1 years ago by
waqasnayab
▴ 250
64
votes
24
replies
3.0k
views
12 follow
Forum:
How much I must feel useless?
machine-learning
Programming
statistics
updated 11 months ago by
Ram
43k • written 5.6 years ago by
Molecular_genetics
▴ 80
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 6 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
159
votes
24
replies
62k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 10 months ago by
Ram
43k • written 11.1 years ago by
Nicolas Rosewick
10k
15
votes
24
replies
2.6k
views
7 follow
Forum:
Airport.bio: First class ticket to any biological database in the world
RNA-Seq
ChIP-Seq
SNP
updated 11 months ago by
Ram
43k • written 6.0 years ago by
Bohdan Khomtchouk
▴ 350
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Pierre Lindenbaum
161k
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Giovanni M Dall'Olio
28k
27
votes
24
replies
2.4k
views
7 follow
Code Golf - bisulfite conversion
bisulfite
bsseq
code-golf
updated 11 months ago by
Ram
43k • written 5.6 years ago by
Chris Miller
22k
4
votes
24
replies
6.0k
views
Split a concatenated alignment in multiple files
alignment
fasta
updated 6 months ago by
Felipe
• 0 • written 9.1 years ago by
dago
★ 2.8k
48
votes
24
replies
8.2k
views
14 follow
Tool:
Hera: A new tool for RNA-Seq analysis
kallisto
RNA-Seq
STAR
gene-fusion
updated 10 months ago by
Ram
43k • written 6.7 years ago by
sonpham
▴ 580
20
votes
24
replies
6.9k
views
6 follow
Forum:
Python or R
RNA-Seq
alignment
next-gen-sequencing
updated 11 months ago by
Ram
43k • written 5.9 years ago by
Qingyang Xiao
▴ 160
66
votes
23
replies
49k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 5 weeks ago by
Getnet Tesfaw
• 0 • written 6.4 years ago by
1769mkc
★ 1.2k
33
votes
23
replies
21k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 7 months ago by
alejandrogzi
▴ 120 • written 6.1 years ago by
JJ
▴ 670
93
votes
23
replies
92k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
18
votes
23
replies
7.7k
views
7 follow
How to exclude some of breast cancer subtypes just by looking at gene expression?
RNA-Seq
genome
cancer
gene
updated 10 months ago by
Safu
• 0 • written 6.4 years ago by
jack
▴ 960
11
votes
23
replies
1.7k
views
gatk Hardfilter Error
hardfilter
updated 10 months ago by
Michael
54k • written 11 months ago by
bestone
▴ 30
40
votes
23
replies
4.1k
views
12 follow
Forum:
Why learn programming in bioinformatics?
Programming
updated 11 months ago by
Ram
43k • written 5.6 years ago by
joselu
▴ 110
23
votes
23
replies
9.8k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 7 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
66
votes
23
replies
10k
views
9 follow
Using Hdf5 To Store Bio-Data
hdf5
storage
database
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Pierre Lindenbaum
161k
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp
amino-acids
updated 3 months ago by
gernophil
▴ 80 • written 12.3 years ago by
Preethi
▴ 110
39
votes
23
replies
34k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 7 months ago by
s.w.vanderlaan
▴ 40 • written 2.8 years ago by
Michal Nevo
▴ 130
61
votes
23
replies
56k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam
mapping
updated 5 months ago by
Lluís R.
★ 1.2k • written 11.2 years ago by
Jordan
★ 1.3k
20
votes
23
replies
7.1k
views
6 follow
Tool:
EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq
Windows
Visualization
ChIP-Seq
updated 10 months ago by
Ram
43k • written 8.1 years ago by
Mads Lerdrup
▴ 460
56
votes
23
replies
5.0k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 10 months ago by
Ram
43k • written 7.8 years ago by
dariober
14k
33
votes
23
replies
4.1k
views
8 follow
Forum:
Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF
file-format
genomics
updated 10 months ago by
Jeremy Leipzig
22k • written 10 months ago by
LauferVA
4.2k
12
votes
23
replies
8.3k
views
6 follow
motif search with ATAC-seq
motif-search
ATAC-seq
updated 10 months ago by
Ram
43k • written 5.5 years ago by
grant.hovhannisyan
★ 2.6k
6
votes
23
replies
26k
views
6 follow
devtools Installation error in R (version 3.5.3)?
github
R
phylogeny
devtools
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Kumar
▴ 120
6
votes
23
replies
1.4k
views
How to speed Salmon index up
metagenome
genome
salmon
3 months ago by
young_bioinformatician
▴ 230
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 15 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
3
votes
22
replies
4.0k
views
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
GRanges
updated 10 months ago by
Amitm
★ 2.2k • written 14 months ago by
Antonia
• 0
1
vote
22
replies
2.0k
views
error with Tximport when txOut = TRUE
tximport
R
updated 9 months ago by
Ram
43k • written 9 months ago by
mbansal
• 0
31
votes
22
replies
13k
views
6 follow
Tool:
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ
SeqKit
FASTA
updated 10 months ago by
Ram
43k • written 7.6 years ago by
shenwei356
8.4k
26
votes
22
replies
13k
views
10 follow
Tool:
BBSketch - A Tool for Rapid Sequence Comparison
minhash
sketch
bbmap
blast
updated 11 months ago by
Ram
43k • written 7.2 years ago by
Brian Bushnell
20k
15
votes
22
replies
8.6k
views
What Are The Most Reliable Normalization Methods For Microarrays?
microarray
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Jarretinha
3.4k
34
votes
22
replies
2.9k
views
11 follow
Forum:
Have we failed as bioinformatician in this time of COVID-19
Bioinformatician
COVID-19
updated 10 months ago by
Ram
43k • written 4.0 years ago by
heididunst
▴ 10
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
5
votes
22
replies
12k
views
sra toolkit program fastq-dump question.
sratoolkit
fastq-dump
updated 10 months ago by
Ram
43k • written 9.2 years ago by
jinhwa1112
▴ 10
28
votes
22
replies
57k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r
genomics
entrez
updated 10 months ago by
cwang3444
• 0 • written 11.0 years ago by
grosy
▴ 90
11
votes
22
replies
4.6k
views
7 follow
Which New Bioinformatics Related Tool Would You Appreciate The Most?
programming
updated 10 months ago by
Ram
43k • written 11.8 years ago by
Biomonika (Noolean)
3.2k
12
votes
22
replies
1.8k
views
Can anyone simplify GATK installation
GATK
3 months ago by
Tundup
• 0
24
votes
22
replies
27k
views
11 follow
replace fasta headers with another name in a text file
perl
updated 9 months ago by
nr299
• 0 • written 9.9 years ago by
Jemo
▴ 60
1,000 results • Page
3 of 20
Recent Votes
Comment: 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)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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▴ 10
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★ 2.5k
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daffodil
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Recent Replies
Answer: 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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