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1,000 results • Page 2 of 20
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93
votes
19
replies
57k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 3 months ago by 40k • written 13.1 years ago by ★ 2.6k
76
votes
24
replies
57k
views
16 follow
How To Sort Bed Format File
bed
updated 11 months ago by 157k • written 10.6 years ago by ▴ 450
131
votes
22
replies
57k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 3 months ago by 86k • written 5.9 years ago by ★ 1.9k
85
votes
2
replies
56k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 7 months ago by 40k • written 10.3 years ago by 11k
28
votes
22
replies
53k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 3 months ago by • 0 • written 10.4 years ago by ▴ 90
146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 7 months ago by 40k • written 10.5 years ago by 6.0k
1.2k
votes
206
replies
52k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 3 months ago by ★ 1.2k • written 12.5 years ago by 21k
76
votes
22
replies
52k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 6 months ago by 40k • written 9.6 years ago by ★ 1.5k
49
votes
13
replies
52k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 7 hours ago by ▴ 140 • written 7.7 years ago by ▴ 490
40
votes
9
replies
51k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 8 weeks ago by ▴ 140 • written 3.8 years ago by ▴ 140
48
votes
19
replies
51k
views
11 follow
How Can I Convert Bam/Sam To Wiggle
wiggle perl samtools
updated 6 months ago by 40k • written 13.0 years ago by ★ 1.4k
0
votes
3
replies
50k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
66
votes
19
replies
48k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 3 months ago by 40k • written 10.6 years ago by ★ 3.6k
35
votes
5
replies
48k
views
Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about that in an assymmetrical matrix
pheatmap R
updated 7 months ago by 40k • written 6.6 years ago by ▴ 180
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 months ago by 40k • written 10.3 years ago by ★ 3.0k
46
votes
15
replies
48k
views
11 follow
How to extract specific chromosome from vcf file
vcf
updated 11 months ago by ▴ 550 • written 7.2 years ago by ★ 2.0k
52
votes
21
replies
47k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 3 months ago by 40k • written 11.5 years ago by ★ 1.5k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 4 weeks ago by ▴ 260 • written 5.8 years ago by 86k
27
votes
15
replies
46k
views
16 follow
how to unzip the files in batch?
next-gen RNA-Seq SNP alignment
updated 7 months ago by 40k • written 8.4 years ago by ▴ 50
125
votes
46
replies
46k
views
21 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 5 months ago by 40k • written 7.6 years ago by ★ 3.2k
54
votes
52
replies
46k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 3 months ago by 40k • written 9.1 years ago by 7.5k
2
votes
5
replies
45k
views
Convert text file to VCF file ?
vcf
updated 3 months ago by 40k • written 8.6 years ago by ▴ 260
32
votes
19
replies
45k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 11 weeks ago by 40k • written 10.3 years ago by ▴ 240
118
votes
74
replies
44k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 11 months ago by 134k • written 12.8 years ago by ★ 3.3k
32
votes
10
replies
43k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat illumina strand
updated 11 months ago by 40k • written 10.6 years ago by 10k
23
votes
22
replies
43k
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 10 months ago by • 0 • written 5.4 years ago by ▴ 250
5
votes
7
replies
43k
views
PLINK: merge .bed files
plink
updated 9 months ago by 40k • written 8.3 years ago by ▴ 230
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 7 months ago by 40k • written 8.4 years ago by ★ 2.0k
31
votes
11
replies
43k
views
9 follow
How To Sort Sam File
samtools sam
updated 8 months ago by 40k • written 9.6 years ago by ★ 1.1k
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 77k
53
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 7 months ago by 40k • written 11.5 years ago by 11k
26
votes
9
replies
42k
views
How Logfc Value Is Calculated In Edger?
edger r RNA-seq
updated 7 months ago by 40k • written 10.0 years ago by ▴ 240
33
votes
11
replies
42k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 7 months ago by 40k • written 11.4 years ago by ▴ 160
39
votes
17
replies
41k
views
13 follow
Extract Cds Fastas From A Gff Annotation + Reference Sequence
gff CDS
updated 7 months ago by 40k • written 11.3 years ago by ▴ 710
60
votes
52
replies
41k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 months ago by 40k • written 7.0 years ago by ★ 3.3k
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 9 days ago by 11k • written 10.7 years ago by ▴ 810
8
votes
12
replies
40k
views
8 follow
Tools to view fastq file
fastq
updated 3 months ago by 40k • written 7.4 years ago by ▴ 40
44
votes
9
replies
40k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 5 months ago by ▴ 30 • written 6.8 years ago by ★ 1.2k
121
votes
35
replies
40k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 4 months ago by 40k • written 6.3 years ago by ▴ 790
62
votes
24
replies
40k
views
12 follow
How to extract unique mapped results from Bowtie2 bam results?
alignment
updated 9 months ago by 40k • written 9.3 years ago by ▴ 170
81
votes
21
replies
40k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 13 days ago by ▴ 180 • written 9.6 years ago by ▴ 750
52
votes
14
replies
40k
views
13 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 3 months ago by 40k • written 13.5 years ago by ▴ 660
35
votes
13
replies
39k
views
8 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 4 months ago by ▴ 80 • written 7.2 years ago by ★ 5.2k
206
votes
58
replies
39k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 7 months ago by 40k • written 10.4 years ago by 9.7k
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
34
votes
8
replies
39k
views
9 follow
Difference Between "Mate Pair" And "Pair-End"
paired-end ngs library
updated 9 months ago by ★ 3.2k • written 10.2 years ago by ▴ 130
28
votes
14
replies
39k
views
8 follow
Running and Analyzing fastqc on multiple fastq files
next-gen RNA-Seq genome
updated 7 months ago by 40k • written 8.4 years ago by ▴ 220
14
votes
2
replies
39k
views
what is difference between sequence adapter and PCR primer?
adapter pcr
updated 8 months ago by 40k • written 8.3 years ago by ▴ 110
58
votes
25
replies
38k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 6 months ago by 40k • written 7.2 years ago by ★ 9.3k
20
votes
12
replies
38k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
perl python awk
updated 7 months ago by 40k • written 9.8 years ago by 9.7k
1,000 results • Page 2 of 20
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Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
A: What'S The Difference Between Cds And Orf?
What'S The Difference Between Cds And Orf?
Answer: Filtering transcription factor and HOMER and ENCODE
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
Answer: Number of accessible regions included by DESeq2 to generate the PCA plot with th
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Recent Replies
Answer: Have some issues in running prokka on WSL by Philipp Bayer 7.9k
It looks like the conda-installed BLAST has issues with the system's ZSTD, which is probably some WSL weirdness. You *might* be able to fix…
Comment: Network analysis with cytoscape by Chris ▴ 180
Sure, the network represents the different expressed genes in my RNA-seq. I choosed string protein query.
Comment: Network analysis with cytoscape by Yogi ▴ 40
A few questions. 1. What does the network represent? 2. Can you insert a high level picture of the network (or pictures) if you want to zo…
Answer: Chip-Seq and correlation of bam file by jared.andrews07 ★ 15k
Use [deepTools' plotCorrelation function](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html).
Answer: Transcription factor co-localization p-values by jared.andrews07 ★ 15k
[regioneR](https://bioconductor.org/packages/release/bioc/html/regioneR.html) seems to be what you want.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data by LChart 3.4k
> Our major biological questions are: to have a general comparison of cancer vs normal “treatment” conditions; In addition if doable, to co…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thanks @luffy! Great material but seem they didn't mention how to customize the background genes depend on our data.
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM by camillab. ▴ 140
I have calculate from this [tutorial][1]. so basically it retrieve the normalized counts matrix using `Deseq2` . Do you think it is correct…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by GenoMax 134k
`dorado` can't demultiplex data as yet (v.0.3.4). Also no adapter trimming. So something to keep in mind if you are switching. To address …
Comment: Frustrated with DEA results by dsull ★ 4.7k
Let the data speak. If there's no difference, then there's no difference. Human clinical data is always messy and unpredictable, especiall…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Ram 40k
I don't think they bought the Mac Studio just for the MiniON. If they did, that might be overkill. All things considered, I'd prefer an App…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by ATpoint 77k
Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation f…
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Christopher ▴ 10
I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequenci…
Comment: ncbi error report log for validate fastq issue by GenoMax 134k
You may want to use `--split-files` instead. With your `--split-spot` option looks like you end up with interleaved data files. Unless you …
Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor by Ram 40k
Nope, I kinda gave up. I got to the image on what fragment size is (https://www.biostars.org/p/106291/#106344) but cannot figure out how to…
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