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187 results • Page
4 of 4
Sort: Rank
Rank
Views
Votes
Replies
2
votes
5
replies
453
views
Marking duplicates using UMIs
Deduplication
UMI
updated 4 days ago by
i.sudbery
19k • written 6 days ago by
Lipika
• 0
0
votes
0
replies
139
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 5 days ago by
Ram
43k • written 6 days ago by
sainavyav22
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
6 days ago by
rthapa
▴ 90
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
6 days ago by
Mamatha Y S
• 0
0
votes
0
replies
131
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 5 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
524
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 6 days ago by
ATpoint
82k • written 7 days ago by
rheab1230
▴ 140
0
votes
2
replies
262
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
7
votes
6
replies
476
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
5 days ago by
analyst
▴ 30
1
vote
1
reply
258
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Bioinformatician
• 0
1
vote
0
replies
542
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
6 days ago by
mathavanbioinfo
▴ 90
2
votes
5
replies
524
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 6 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
Giorgio
• 0
0
votes
0
replies
214
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
6 days ago by
abhishekghadge
• 0
2
votes
5
replies
688
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 6 days ago by
Jesse
▴ 740 • written 7 days ago by
Ann
★ 2.4k
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 6 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
5
votes
13
replies
1.2k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 6 days ago by
ATpoint
82k • written 7 days ago by
BioinfGuru
★ 1.7k
3
votes
4
replies
661
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
4 days ago by
rahu
• 0
3
votes
3
replies
471
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 8 days ago by
joe
▴ 510
0
votes
0
replies
203
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
4 days ago by
Javier
• 0
1
vote
1
reply
419
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
Chris
▴ 260
0
votes
0
replies
192
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
3
votes
6
replies
650
views
Ciriquant not configuring hisat2 indexed files
ciriquant
5 days ago by
Atul K.
• 0
1
vote
2
replies
235
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 18 days ago by
Netanel
• 0
0
votes
6
replies
431
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 2 days ago by
gv
• 0 • written 25 days ago by
Srinka
▴ 20
4
votes
2
replies
372
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 1 day ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
0
votes
2
replies
584
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 days ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
1
vote
5
replies
591
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 3 days ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
1
vote
4
replies
423
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 3 days ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
2
votes
3
replies
948
views
Method to detect genome doubling
CNV
genome doubling
updated 4 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
0
votes
0
replies
274
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 4 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 1 day ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 1 day ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 1 day ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 3 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 20 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 6 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 2 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 5 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
187 results • Page
4 of 4
Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Recent Awards •
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Scholar
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Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
Commentator
to
GenoMax
141k
Popular Question
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rheab1230
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BioinfGuru
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bk11
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vinayjrao
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Recent Replies
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
by
dsull
★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
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