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13,540 results • Page
2 of 271
Sort: Views
Rank
Views
Votes
Replies
48
votes
9
replies
44k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 3 months ago by
Picasa
▴ 640 • written 7.5 years ago by
ZheFrench
▴ 570
121
votes
35
replies
43k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 11 months ago by
Ram
43k • written 6.9 years ago by
ropolocan
▴ 810
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 7 months ago by
zx8754
11k • written 11.3 years ago by
henryvuong
▴ 810
81
votes
21
replies
43k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 7 months ago by
Joel Wallenius
▴ 210 • written 10.2 years ago by
pristanna
▴ 750
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 2 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing
fastq
updated 5 months ago by
Pierre Lindenbaum
161k • written 14.0 years ago by
Zach Stednick
▴ 660
121
votes
33
replies
39k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by
carlopecoraro2
★ 2.5k • written 10.7 years ago by
Eric Normandeau
11k
6
votes
25
replies
39k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 11 months ago by
13554221497
• 0 • written 6.1 years ago by
ARich
▴ 130
23
votes
4
replies
38k
views
bcftools compressing and indexing vcf files
sequence
bcftools
vcf
index
updated 5 months ago by
GenoMax
142k • written 5.7 years ago by
Inquisitive8995
▴ 270
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by
Axzd
▴ 70 • written 9.8 years ago by
onter
▴ 170
19
votes
10
replies
38k
views
Ensembl ID to Gene Symbol
gene-symbol
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
13
votes
6
replies
37k
views
generating genome indexes with STAR
RNA-Seq
STAR
updated 9 months ago by
DareDevil
★ 4.3k • written 7.9 years ago by
snp87
▴ 80
10
votes
5
replies
37k
views
How to compare 2 VCF files
vcf
SNP
updated 10 months ago by
Ram
43k • written 10.0 years ago by
Parimala Devi
▴ 100
21
votes
8
replies
37k
views
8 follow
Merging/Concatenating Vcf Files
vcftools
snp
indel
updated 8 months ago by
Bioinformatics_NewComer
▴ 330 • written 11.7 years ago by
bioinfo
▴ 830
80
votes
21
replies
37k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by
kathryn.jacksonjones
• 0 • written 10.0 years ago by
M K
▴ 660
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
142k • written 3.7 years ago by
lavinia.gordon
▴ 160
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq
macs
ChIP-Seq
peaks
updated 10 months ago by
Ram
43k • written 7.7 years ago by
igor
13k
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing
duplicates
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
161k
33
votes
10
replies
35k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq
ensembl
updated 9 months ago by
Ram
43k • written 9.8 years ago by
pwg46
▴ 540
197
votes
27
replies
35k
views
20 follow
Forum:
Bioinformatics Cartoon
bioinformatics
updated 9 months ago by
Ram
43k • written 12.3 years ago by
Maxime Lamontagne
★ 2.3k
20
votes
10
replies
35k
views
6 follow
read depth using samtools
depth
samtools
updated 7 months ago by
Sachin
▴ 10 • written 5.3 years ago by
LimMo
▴ 30
13
votes
12
replies
34k
views
Estimating Insert Size From Paired End Data.
picard
alignment
paired-end
updated 7 months ago by
Ram
43k • written 10.2 years ago by
GouthamAtla
12k
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 8 months ago by
s.w.vanderlaan
▴ 40 • written 2.8 years ago by
Michal Nevo
▴ 130
28
votes
11
replies
34k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools
strand
updated 3 months ago by
shaoqian ma
• 0 • written 12.5 years ago by
Gregor Rot
▴ 540
42
votes
16
replies
34k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 7 months ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
chparada
▴ 70
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
67
votes
15
replies
33k
views
14 follow
Rna-Seq Pipeline
pipeline
next-gen-sequencing
rna
rna-seq
updated 11 months ago by
Ram
43k • written 14.0 years ago by
brentp
24k
298
votes
122
replies
33k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 8 months ago by
jena
▴ 290 • written 13.8 years ago by
Eric Normandeau
11k
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 8 weeks ago by
nickp60
▴ 60 • written 7.9 years ago by
andrew.j.skelton73
6.6k
36
votes
11
replies
33k
views
6 follow
Sjdboverhang Option In Star
updated 9 months ago by
Kermit
▴ 90 • written 10.2 years ago by
Martombo
★ 3.1k
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
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter
sequence
human
genome
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Yuri
★ 1.7k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
20
votes
9
replies
32k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart
r
bioconductor
updated 12 months ago by
Kevin Blighe
87k • written 11.8 years ago by
sthait
▴ 120
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
79
votes
86
replies
32k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 10 months ago by
Ram
43k • written 7.4 years ago by
Brian Bushnell
20k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner
snp
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
72
votes
71
replies
31k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot
bioconductor
ggplot2
ggrepel
updated 10 months ago by
Ram
43k • written 5.7 years ago by
Kevin Blighe
87k
14
votes
8
replies
31k
views
NarrowPeak format of ChiP-seq
ChIP-Seq
tag-density
updated 10 months ago by
minakshiboruahassam
• 0 • written 9.9 years ago by
liu4gre
▴ 210
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 23 days ago by
Jeremy Leipzig
22k • written 10.5 years ago by
14134125465346445
★ 3.6k
28
votes
16
replies
31k
views
11 follow
How Do I Convert From Bed Format To Gff Format?
gff
galaxy
bed
updated 6 months ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
130
votes
19
replies
31k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq
alignment
next-gen
R
assembly
updated 3 months ago by
Ram
43k • written 4.6 years ago by
WUSCHEL
▴ 750
4
votes
9
replies
31k
views
8 follow
How To Get Chromosome Position Given Rs Number?
snp
chromosome
position
updated 5 months ago by
GenoMax
142k • written 10.5 years ago by
chrismas05
• 0
23
votes
12
replies
30k
views
9 follow
Extract Alignment From Very Large Bam File
bam
updated 3 months ago by
Ram
43k • written 11.9 years ago by
Plantae
▴ 390
25
votes
11
replies
30k
views
9 follow
Bed For Agilent Sureselect All Exon Kits ?
bed
exome
agilent
next-gen
written 11.4 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
54
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 9 months ago by
DareDevil
★ 4.3k • written 10.8 years ago by
user
▴ 940
13
votes
3
replies
29k
views
What is the difference between blastx and tblastn?
assembly
blast
ncbi
sequence
updated 11 months ago by
Ram
43k • written 4.9 years ago by
Kumar
▴ 120
57
votes
22
replies
29k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 26 days ago by
Ram
43k • written 4.6 years ago by
Arindam Ghosh
▴ 510
19
votes
9
replies
28k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis
RNA-Seq
ngs
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Arindam Ghosh
▴ 510
13,540 results • Page
2 of 271
Recent Votes
A: Decoy In Reference Assembly
A: Decoy In Reference Assembly
Decoy In Reference Assembly
Decoy In Reference Assembly
Comment: Bacterial plasmid analysis
Unsupervised clustering on gene expression data
Answer: Bacterial plasmid analysis
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Recent Replies
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
GenoMax
142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
Begonia_pavonina
▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq
by
GenoMax
142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
Comment: Bacterial plasmid analysis
by
Daria
▴ 10
I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Ok I think I know what happened. The order of cells changed, otherwise its the same: ![image](https://github.com/satijalab/seurat/assets/7…
Answer: Bacterial plasmid analysis
by
shenwei356
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…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
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…
Comment: Odd alignment question/finding
by
liorglic
★ 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…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
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