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1,000 results • Page
5 of 20
Sort: Views
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Views
Votes
Replies
4
votes
1
reply
48k
views
In ggplot, assign a variable/category to a specific color?
R
ggplot
plots
colors
updated 7.6 years ago by
Biostar
20 • written 7.8 years ago by
james.lloyd
▴ 100
30
votes
10
replies
48k
views
Filtering A Sam File For Quality Scores
sam
updated 12.0 years ago by
Sukhi Singh
11k • written 12.0 years ago by
Varun Gupta
★ 1.3k
39
votes
14
replies
48k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl
fasta
python
parsing
updated 2.0 years ago by
Michael
54k • written 12.3 years ago by
Mohammad Reza Bakhtiarizadeh
▴ 350
24
votes
14
replies
48k
views
7 follow
Gene symbol convert to Entrez ID
Entrez
R
biomart
updated 5.6 years ago by
zx8754
11k • written 6.9 years ago by
landscape95
▴ 190
3
votes
5
replies
48k
views
Convert text file to VCF file ?
vcf
updated 10 months ago by
Ram
43k • written 9.2 years ago by
CrazyB
▴ 280
32
votes
8
replies
47k
views
7 follow
Difference Between "Pipeline" And "Workflow" ?
next-gen
sequencing
written 12.2 years ago by
Pascal
★ 1.5k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 9 months ago by
Ram
43k • written 10.9 years ago by
hicsuntdrac0nis
▴ 250
6
votes
12
replies
47k
views
9 follow
Opening A Fasta File In Windows
fasta
blast
makeblastdb
updated 12.2 years ago by
Vivek
• 0 • written 12.2 years ago by
Vivek
• 0
22
votes
4
replies
47k
views
Convert plink files to VCF: Reference allele file
SNP
genome
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Ishtiaq Ahmad Khan
▴ 70
49
votes
4
replies
47k
views
How To Convert The Bed File To Ped File
bed
ped
updated 20 months ago by
sonsunjirachote
• 0 • written 13.7 years ago by
Austinlew
▴ 310
112
votes
24
replies
47k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp
samtools
alignment
next-gen
sequencing
updated 20 months ago by
Ram
43k • written 13.0 years ago by
Matthieu
▴ 480
99
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 24 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
118
votes
74
replies
46k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 18 months ago by
GenoMax
142k • written 13.4 years ago by
Casbon
★ 3.3k
57
votes
23
replies
46k
views
14 follow
Bam File: Change Chromosome Notation
samtools
bam
updated 2.9 years ago by
zx8754
11k • written 12.5 years ago by
Lisanne
▴ 160
77
votes
18
replies
46k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 21 months ago by
Dan
• 0 • written 14.0 years ago by
Science_Robot
★ 1.1k
117
votes
66
replies
46k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 13 months ago by
Ram
43k • written 5.8 years ago by
ATpoint
82k
17
votes
5
replies
46k
views
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
heatmap
r
updated 12.4 years ago by
Michael
54k • written 12.4 years ago by
C Shao
▴ 140
9
votes
12
replies
46k
views
8 follow
Tools to view fastq file
fastq
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Roden Luo
▴ 40
11
votes
8
replies
46k
views
Converting Smiles To Iupac Chemical Name?
updated 11.8 years ago by
Egon Willighagen
5.4k • written 11.8 years ago by
dimkal
▴ 730
81
votes
6
replies
45k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam
samtools
next-gen
updated 2.1 years ago by
Ram
43k • written 12.0 years ago by
Stefano Berri
4.4k
49
votes
10
replies
45k
views
When and why is bwa aln better then bwa mem?
aln
comparison
bwa
mem
updated 3.1 years ago by
Ram
43k • written 9.5 years ago by
dariober
14k
298
votes
27
replies
45k
views
33 follow
Forum:
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq
sequencing
papers
updated 21 months ago by
Ram
43k • written 8.3 years ago by
CandiceChuDVM
★ 2.4k
32
votes
7
replies
45k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq
deseq2
tpm
updated 22 months ago by
Ram
43k • written 9.2 years ago by
Tom Harrop
▴ 170
22
votes
7
replies
45k
views
Extracting cells only from one condition (Seurat)
single cell rnaseq
seurat
RNA-Seq
R
updated 3.0 years ago by
Tatyana
▴ 50 • written 4.2 years ago by
V
▴ 380
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 7.9 years ago by
Biostar
20 • written 12.0 years ago by
Sahel
▴ 310
35
votes
11
replies
45k
views
8 follow
Where Can I Download Some Bam Files?
bam
RNA-seq
updated 4 months ago by
Ram
43k • written 12.0 years ago by
snakesgun
▴ 160
134
votes
27
replies
45k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.0 years ago by
Ram
43k • written 12.0 years ago by
lh3
33k
32
votes
11
replies
45k
views
9 follow
How To Sort Sam File
samtools
sam
updated 15 months ago by
Ram
43k • written 10.2 years ago by
Chen Sun
★ 1.1k
25
votes
23
replies
44k
views
12 follow
How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
samtools
next-gen
sequencing
fasta
updated 10.3 years ago by
mobiusklein
▴ 180 • written 13.9 years ago by
Casey Bergman
18k
17
votes
3
replies
44k
views
What'S The Meaning Of "Bridge Pcr" In The Next Generation Sequencing
pcr
sequencing
updated 10.8 years ago by
William
★ 5.3k • written 10.8 years ago by
weiqiangduan
▴ 150
23
votes
8
replies
44k
views
Convert .Txt File To Bed File
bed
updated 9.8 years ago by
inesdesantiago
▴ 260 • written 12.6 years ago by
Bioscientist
★ 1.7k
63
votes
8
replies
44k
views
6 follow
Why Do You Need To Use Cdna For Rna-Seq?
rna-seq
cdna
updated 7.7 years ago by
SeqFreak
• 0 • written 11.6 years ago by
Justin
▴ 460
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 23 months ago by
Ram
43k • written 9.2 years ago by
MAPK
★ 2.1k
25
votes
9
replies
44k
views
Converting Gff To Bed With Bedtools?
gff
bed
bedtools
updated 12 weeks ago by
Ram
43k • written 11.3 years ago by
user
▴ 940
32
votes
10
replies
44k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat
illumina
strand
updated 18 months ago by
Ram
43k • written 11.2 years ago by
Nicolas Rosewick
11k
112
votes
56
replies
44k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq
next-gen
sequencing
fusion
updated 19 months ago by
Ram
43k • written 11.9 years ago by
KS
▴ 380
85
votes
19
replies
44k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly
quality
next-gen
updated 2.2 years ago by
WANG
▴ 10 • written 11.3 years ago by
diltsjeri
▴ 470
32
votes
5
replies
44k
views
What is Differential Expression?
DNA
genes
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
LoveLeh
▴ 50
35
votes
14
replies
44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf
bcftools
updated 7 months ago by
ashotmarg2004
▴ 130 • written 7.8 years ago by
William
★ 5.3k
3
votes
5
replies
44k
views
how to set the size of cell of heatmap.2 in R
heatmap.2
R
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Zhilong Jia
★ 2.2k
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
53
votes
19
replies
44k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 14 months ago by
Ram
43k • written 12.1 years ago by
Sukhi Singh
11k
60
votes
52
replies
43k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 13 months ago by
Ram
43k • written 7.6 years ago by
steve
★ 3.5k
37
votes
15
replies
43k
views
8 follow
FPKM vs raw counts vs RPKM
counts
rpkm
raw
fpkm
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
NHEJ
▴ 360
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 15 months ago by
Ram
43k • written 9.0 years ago by
MAPK
★ 2.1k
26
votes
9
replies
43k
views
How Logfc Value Is Calculated In Edger?
edger
r
RNA-seq
updated 14 months ago by
Ram
43k • written 10.6 years ago by
nbvasani
▴ 240
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
14
votes
6
replies
43k
views
Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
ncbi
updated 10.7 years ago by
SRKR
▴ 180 • written 10.7 years ago by
bioinfo
▴ 830
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 12 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
63
votes
16
replies
43k
views
11 follow
How To Analyze Imputed Gwas Data
gwas
r
snp
imputation
plink
updated 3.9 years ago by
Mahan
▴ 70 • written 13.1 years ago by
Stephen
2.8k
1,000 results • Page
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Answer: Does comparing two different groups to a common third group introduce bias in th
Comment: High Malat-1 expression in single cell data
Comment: High Malat-1 expression in single cell data
Print Differentially Expressed Exons From Dexseq Results
C: Print Differentially Expressed Exons From Dexseq Results
C: Print Differentially Expressed Exons From Dexseq Results
Answer: Please Explain Window Size and Step Size
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie
by
GenoMax
142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data
by
carolofharvest
▴ 30
Thank you for sharing. What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
Comment: Do I need to go back and filter my long-reads?
by
GenoMax
142k
> I think I will filter the reads ultimately. If your data was not run and basecalled using the same exact version of pore/software for a…
Comment: Raw counts using stringtie
by
Ram
43k
What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
Comment: Do I need to go back and filter my long-reads?
by
Ram
43k
> I think you should have the right to delete a question you yourself have submitted If you were to talk to someone, can you make them for…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★ 1.9k
I don't have any experience using `BRAKER2` so I cannot comment, but I would be extra careful about data you find on non-model organisms. T…
Comment: Differential Expression Analysis using DESeq2 in R
by
GenoMax
142k
You can copy and paste your code and then use `101010` button in the edit window to format it as text to keep it monospaced. For example …
Comment: Same sequencing sample in multiple lanes. How to analyse it?
by
ST
• 0
I guess this could really depend on the "counting" strategy, the library complexity and possible lane biases. If e.g., EM is used to guide…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
Vijith
▴ 30
Hi dthorbur, thanks for the response. I have run Augustus using Arabidopsis as a species. I would like to know about the suitability of usi…
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by
dsull
★ 6.0k
Alicia Oshlack has done some cool work on this but even the plots in her papers show that TPMs sometimes overcorrect and the relationship i…
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by
Erina
• 0
![The below image contains the code and result also.][1] [1]: /media/images/96562b96-d508-4f67-96d1-7c71aa17
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
My response above was actually partly inspired off of a reading of your paper :)
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