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118,118 results • Page 5 of 2363
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102
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107
replies
49k
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27 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 7 weeks ago by • 0 • written 5.9 years ago by 88k
16
votes
8
replies
49k
views
9 follow
Ensembl Ids To Gene Name Conversion
gene ensembl
updated 5.4 years ago by • 0 • written 12.2 years ago by ▴ 30
32
votes
10
replies
49k
views
Filtering A Sam File For Quality Scores
sam
updated 12.2 years ago by 11k • written 12.2 years ago by ★ 1.3k
40
votes
14
replies
49k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl fasta python parsing
updated 2.3 years ago by 54k • written 12.6 years ago by ▴ 350
3
votes
5
replies
49k
views
Convert text file to VCF file ?
vcf
updated 13 months ago by 44k • written 9.4 years ago by ▴ 280
33
votes
8
replies
49k
views
7 follow
Difference Between "Pipeline" And "Workflow" ?
next-gen sequencing
written 12.4 years ago by ★ 1.5k
22
votes
4
replies
49k
views
Convert plink files to VCF: Reference allele file
SNP genome
updated 22 months ago by 44k • written 8.9 years ago by ▴ 70
4
votes
1
reply
48k
views
In ggplot, assign a variable/category to a specific color?
R ggplot plots colors
updated 7.8 years ago by 20 • written 8.0 years ago by ▴ 100
10
votes
12
replies
48k
views
8 follow
Tools to view fastq file
fastq
updated 13 months ago by 44k • written 8.2 years ago by ▴ 40
6
votes
12
replies
48k
views
9 follow
Opening A Fasta File In Windows
fasta blast makeblastdb
updated 12.4 years ago by • 0 • written 12.4 years ago by • 0
34
votes
19
replies
48k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 12 months ago by 44k • written 11.2 years ago by ▴ 250
58
votes
23
replies
48k
views
14 follow
Bam File: Change Chromosome Notation
samtools bam
updated 3.2 years ago by 11k • written 12.8 years ago by ▴ 160
49
votes
4
replies
47k
views
How To Convert The Bed File To Ped File
bed ped
updated 23 months ago by • 0 • written 13.9 years ago by ▴ 310
113
votes
24
replies
47k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 23 months ago by 44k • written 13.2 years ago by ▴ 480
117
votes
66
replies
47k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 16 months ago by 44k • written 6.1 years ago by 84k
118
votes
74
replies
47k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 21 months ago by 144k • written 13.6 years ago by ★ 3.3k
77
votes
18
replies
47k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 24 months ago by • 0 • written 14.2 years ago by ★ 1.1k
11
votes
8
replies
47k
views
Converting Smiles To Iupac Chemical Name?
updated 12.0 years ago by 5.4k • written 12.0 years ago by ▴ 730
81
votes
6
replies
46k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam samtools next-gen
updated 2.4 years ago by 44k • written 12.2 years ago by 4.4k
51
votes
9
replies
46k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 5 months ago by ▴ 650 • written 7.7 years ago by ▴ 580
49
votes
10
replies
46k
views
When and why is bwa aln better then bwa mem?
aln comparison bwa mem
updated 3.3 years ago by 44k • written 9.8 years ago by 14k
17
votes
5
replies
46k
views
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
heatmap r
updated 12.6 years ago by 54k • written 12.6 years ago by ▴ 140
302
votes
27
replies
46k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 24 months ago by 44k • written 8.5 years ago by ★ 2.5k
22
votes
7
replies
46k
views
Extracting cells only from one condition (Seurat)
single cell rnaseq seurat RNA-Seq R
updated 3.2 years ago by ▴ 50 • written 4.5 years ago by ▴ 380
35
votes
11
replies
46k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 7 months ago by 44k • written 12.2 years ago by ▴ 160
134
votes
27
replies
46k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.3 years ago by 44k • written 12.3 years ago by 33k
32
votes
7
replies
46k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq deseq2 tpm
updated 2.1 years ago by 44k • written 9.4 years ago by ▴ 170
30
votes
14
replies
45k
views
9 follow
Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
rna-seq differential expression
updated 8.1 years ago by 20 • written 12.2 years ago by ▴ 310
25
votes
9
replies
45k
views
Converting Gff To Bed With Bedtools?
gff bed bedtools
updated 5 months ago by 44k • written 11.5 years ago by ▴ 940
24
votes
8
replies
45k
views
Convert .Txt File To Bed File
bed
updated 10.1 years ago by ▴ 260 • written 12.9 years ago by ★ 1.7k
112
votes
56
replies
45k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 22 months ago by 44k • written 12.2 years ago by ▴ 380
32
votes
11
replies
45k
views
9 follow
How To Sort Sam File
samtools sam
updated 18 months ago by 44k • written 10.4 years ago by ★ 1.1k
35
votes
14
replies
45k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 9 months ago by ▴ 130 • written 8.1 years ago by ★ 5.3k
85
votes
19
replies
45k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly quality next-gen
updated 2.5 years ago by ▴ 10 • written 11.5 years ago by ▴ 470
20
votes
4
replies
45k
views
what does a log 2-fold change values of mean ?
motif microarray gene genesequencing sequencing
5.7 years ago by a4appy23 ▴ 50
25
votes
23
replies
45k
views
12 follow
How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
samtools next-gen sequencing fasta
updated 10.5 years ago by ▴ 180 • written 14.1 years ago by 18k
60
votes
52
replies
45k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 16 months ago by 44k • written 7.8 years ago by ★ 3.5k
123
votes
35
replies
45k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 14 months ago by 44k • written 7.1 years ago by ▴ 820
32
votes
10
replies
45k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat illumina strand
updated 21 months ago by 44k • written 11.4 years ago by 11k
63
votes
8
replies
45k
views
6 follow
Why Do You Need To Use Cdna For Rna-Seq?
rna-seq cdna
updated 7.9 years ago by • 0 • written 11.8 years ago by ▴ 460
17
votes
3
replies
45k
views
What'S The Meaning Of "Bridge Pcr" In The Next Generation Sequencing
pcr sequencing
updated 11.1 years ago by ★ 5.3k • written 11.1 years ago by ▴ 150
19
votes
6
replies
44k
views
How can I convert -log10 (p-value) to p-value?
p-value
updated 21 months ago by ★ 1.2k • written 5.5 years ago by ▴ 80
5
votes
3
replies
44k
views
Extract the values by matching two rows of one dataframe with the two columns of another dataframe
dataframe match
updated 2.2 years ago by 44k • written 9.4 years ago by ★ 2.1k
40
votes
10
replies
44k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 12 weeks ago by ▴ 40 • written 7.0 years ago by ★ 1.4k
3
votes
5
replies
44k
views
how to set the size of cell of heatmap.2 in R
heatmap.2 R
updated 2.4 years ago by 44k • written 9.6 years ago by ★ 2.2k
46
votes
9
replies
44k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 15 months ago by ▴ 50 • written 7.6 years ago by ★ 1.2k
37
votes
15
replies
44k
views
8 follow
FPKM vs raw counts vs RPKM
counts rpkm raw fpkm RNA-Seq
updated 2.4 years ago by 44k • written 9.6 years ago by ▴ 360
32
votes
5
replies
44k
views
What is Differential Expression?
DNA genes
updated 2.6 years ago by 44k • written 9.9 years ago by ▴ 50
53
votes
19
replies
44k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 17 months ago by 44k • written 12.3 years ago by 11k
18
votes
21
replies
44k
views
11 follow
R org.Hs.eg.db matching ensembl gene ids with gene symbol
bioconductor R
updated 2.8 years ago by ▴ 10 • written 8.4 years ago by ▴ 330
118,118 results • Page 5 of 2363
Recent Votes
Now available for download: New, more efficient BLAST core_nt database
Join command for the issue
C: Has anyone run Phobius locally? Error - could not read provided fasta sequences
A: VCF files: Change Chromosome Notation
Comment: Unexpected strandness using salmon
Comment: BRAKER3 genome annotation
A: How to make an intronic GTF for alignment
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Recent Replies
Comment: EditingSites for mm39 by ATpoint 84k
What are "editing sites" in the context of a reference genome?
Comment: Has anyone run Phobius locally? Error - could not read provided fasta sequences by Adrian • 0
Hi! This L25 substitution does work! Huge thanks!
Answer: Enrichment analysis guide for msu7 rice genome by 白 • 0
Did you solve this problem? If you had solved it , please tell me . Hope recieve your reply. Thank you !
Comment: Getting A List Of Pfam Domains Involved in DNA-binding by Tze Jet • 0
Thanks for the reply. However, I would also like the domains that do not have dna-binding in their description, but still may bind to DNA (…
Answer: Merging two sequencing datasets by swbarnes2 14k
I would be wary of combining data from two separate library preps.
Comment: Samtools flagstat output said there is zero paired-reads in scRNA-seq bam file by swbarnes2 14k
People don't always have control over the runs their samples go on. If you have to share a run with other paired samples that needs a 2x15…
Comment: Getting A List Of Pfam Domains Involved in DNA-binding by GenoMax 144k
Search ""dna binding". Export the table as TSV from https://www.ebi.ac.uk/interpro/search/text/ Filter for PFAM, if you only need those.
Answer: Merging two sequencing datasets by rfran010 ★ 1.3k
I say map and QC them separately to determine any batch differences. Then decide to merge them or not (you can merge the bams). Details may…
Comment: Absolute counts or relative abundance for BC distance matrix by Ram 44k
Please do not use `bioinformatics` as a tag unless your post is about the field of bioinformatics itself. For proper examples, please see F…
Answer: Don't understand three modes of TCGA STAR 2-pass by Zhenyu Zhang ★ 1.2k
1. gencode 36 now 2. there are splice junction files 3. genomic alignment is not dependent on gene model
Comment: temp directory as output in snakemake by Jesse ▴ 770
Yep, this behavior is easy to confirm with a couple of test rules and something like `shell: "sleep 60"` in the last one, so you can see th…
Comment: How to use GFF3 annotation to split genome fasta into gene sequence fasta in R by Michael 54k
While this looks as if it works fine, you should look into the vectorized [getSeq method][1] which allows to specify all coodinates at once…
Comment: Finding novel transcripts by biofalconch ★ 1.1k
I encourage you to have a look at OrthoFinder: https://github.com/davidemms/OrthoFinder Not only will you now which transcripts are new, y…
Answer: How to use GFF3 annotation to split genome fasta into gene sequence fasta in R by dthorbur ★ 2.2k
Learning how to implement positive controls is extremely useful in bioinformatics. In this instance, I'm sure you can find some important g…
Comment: is that statistical correct to use DEseq2 for proteomics data by QX ▴ 50
thank you!
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