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1,000 results • Page
3 of 20
Sort: Views
Rank
Views
Votes
Replies
46
votes
9
replies
40k
views
9 follow
How To Convert Centimorgan To Base Pair
genetics
distance
updated 8 months ago by
Ram
39k • written 11.4 years ago by
Aurgha
▴ 90
23
votes
22
replies
40k
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 6 months ago by
Nicole
• 0 • written 5.1 years ago by
gaelgarcia
▴ 250
60
votes
52
replies
40k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 11 weeks ago by
Ram
39k • written 6.7 years ago by
steve
★ 3.3k
105
votes
26
replies
39k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 8 months ago by
Ram
39k • written 10.4 years ago by
henryvuong
▴ 810
14
votes
6
replies
39k
views
7 follow
How To Convert A Fasta Or Alignment File To Nexus (.Nex) File That Is To Be Used In The Beast Program
updated 9 months ago by
kamiljaron
▴ 210 • written 9.8 years ago by
triinlakspere
▴ 20
62
votes
24
replies
39k
views
12 follow
How to extract unique mapped results from Bowtie2 bam results?
alignment
updated 5 months ago by
Ram
39k • written 9.0 years ago by
zhwjmch
▴ 170
206
votes
58
replies
39k
views
31 follow
Forum:
Will Python Take The Place Of R?
r
statistics
python
biopython
updated 3 months ago by
Ram
39k • written 10.0 years ago by
Medhat
9.6k
34
votes
8
replies
38k
views
9 follow
Difference Between "Mate Pair" And "Pair-End"
paired-end
ngs
library
updated 5 months ago by
cmdcolin
★ 3.0k • written 9.9 years ago by
weiqiangduan
▴ 130
28
votes
14
replies
38k
views
8 follow
Running and Analyzing fastqc on multiple fastq files
next-gen
RNA-Seq
genome
updated 4 months ago by
Ram
39k • written 8.1 years ago by
ravi.uhdnis
▴ 220
44
votes
9
replies
38k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 7 weeks ago by
Charles-Alexandre Roy
▴ 30 • written 6.5 years ago by
Abdul Rafay Khan
★ 1.2k
115
votes
35
replies
38k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 23 days ago by
Ram
39k • written 6.0 years ago by
ropolocan
▴ 760
14
votes
2
replies
38k
views
what is difference between sequence adapter and PCR primer?
adapter
pcr
updated 5 months ago by
Ram
39k • written 8.0 years ago by
xiangwulu
▴ 110
20
votes
12
replies
37k
views
7 follow
Forum:
When To Use Sed Awk Over Perl Or Python
perl
python
awk
updated 3 months ago by
Ram
39k • written 9.4 years ago by
Medhat
9.6k
34
votes
13
replies
37k
views
8 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf
bcftools
updated 7 days ago by
Kermit
▴ 80 • written 6.9 years ago by
William
★ 5.2k
58
votes
25
replies
37k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 11 weeks ago by
Ram
39k • written 6.9 years ago by
Shicheng Guo
★ 9.3k
26
votes
12
replies
37k
views
7 follow
Log2 Ratio or Log2 Fold Change - terminology confusion and which one should I use?
genome
updated 10 months ago by
obidobi
▴ 30 • written 6.6 years ago by
Genosa
▴ 150
120
votes
33
replies
36k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 27 days ago by
carlopecoraro2
★ 2.3k • written 9.8 years ago by
Eric Normandeau
11k
50
votes
17
replies
36k
views
17 follow
How To Get Number Of Reads In Bam File Efficiently In Python?
python
samtools
next-gen
sequencing
updated 7 months ago by
Ram
39k • written 12.9 years ago by
User 9996
▴ 840
92
votes
105
replies
36k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 11 weeks ago by
Ram
39k • written 4.8 years ago by
Kevin Blighe
85k
41
votes
17
replies
36k
views
15 follow
Forum:
List Of Genome Sequencing Centers/Institutes
genomics
institutes
updated 3 months ago by
Ram
39k • written 10.3 years ago by
Malachi Griffith
19k
27
votes
13
replies
36k
views
10 follow
Survival Analysis Using Tcga Data
tcga
bioinformatician
updated 3 months ago by
Ram
39k • written 9.2 years ago by
jack
▴ 520
45
votes
2
replies
36k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 3 months ago by
Ram
39k • written 11.2 years ago by
MSU course 2011
▴ 540
46
votes
20
replies
36k
views
13 follow
Counting Number Of Bases In A Fastq File
fastq
ngs
updated 10 months ago by
Der
• 0 • written 9.8 years ago by
DoubleDecker
▴ 180
21
votes
18
replies
36k
views
10 follow
Combining Data Of Multiple Vcfs Into One.
vcf
variant-calling
written 10.0 years ago by
Sheila
▴ 410
60
votes
12
replies
35k
views
10 follow
Get chromosome sizes from fasta file
genome
ucsc
updated 7 months ago by
jamesogilvie1
• 0 • written 7.4 years ago by
rioualen
▴ 700
16
votes
7
replies
35k
views
6 follow
hg38 annotation file (gtf) UCSC format
RNA-Seq
alignment
updated 10 months ago by
Ram
39k • written 7.4 years ago by
dina.hesham139
▴ 160
12
votes
4
replies
35k
views
Forum:
BWA command guide
BWA
updated 3 months ago by
Ram
39k • written 5.3 years ago by
Chen Sun
★ 1.1k
59
votes
36
replies
35k
views
27 follow
Pca From Vcf Files
pca
genome
vcf
updated 10 months ago by
hewm2008
▴ 40 • written 11.1 years ago by
Rubal7
▴ 820
33
votes
12
replies
35k
views
7 follow
How Can I Count Snps In My Vcf Files?
vcf
snp
awk
updated 8 months ago by
Ram
39k • written 10.9 years ago by
Matt W
▴ 250
52
votes
11
replies
34k
views
8 follow
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
RNA-Seq
updated 4 months ago by
Ram
39k • written 8.9 years ago by
thisismytest3023
▴ 210
12
votes
10
replies
34k
views
9 follow
How To Convert Vcf File To Plink Ped Format?
vcftools
updated 8 months ago by
Ram
39k • written 12.3 years ago by
Ketan Padiya
▴ 40
27
votes
4
replies
34k
views
Raw counts to TPM in R
RNA-Seq
R
updated 12 months ago by
ATpoint
72k • written 4.8 years ago by
firestar
★ 1.5k
13
votes
3
replies
33k
views
Drawing venn diagram in R
ChIP-Seq
venn-diagram
updated 10 weeks ago by
Ram
39k • written 8.1 years ago by
Rashedul Islam
▴ 450
33
votes
8
replies
33k
views
9 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 9 weeks ago by
Rene
▴ 10 • written 6.6 years ago by
ZheFrench
▴ 500
18
votes
6
replies
33k
views
How can I convert -log10 (p-value) to p-value?
p-value
updated 7 months ago by
1769mkc
★ 1.1k • written 4.4 years ago by
somayeh bakhshalizadeh
▴ 80
118
votes
26
replies
33k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 12 weeks ago by
e.r.zakiev
▴ 50 • written 8.0 years ago by
mhockin
▴ 610
22
votes
13
replies
33k
views
11 follow
nr- protein database
blast
Assembly
next-gen-sequencing
updated 8 months ago by
Ram
39k • written 7.8 years ago by
Eva_Maria
▴ 190
6
votes
6
replies
33k
views
Can the code of a R package be changed? How?
R
updated 5 months ago by
Ram
39k • written 8.0 years ago by
Antonio R. Franco
★ 5.1k
40
votes
10
replies
33k
views
7 follow
Can'T Locate Vcf.Pm Vcftools
vcftools
vcf
updated 4 months ago by
Ram
39k • written 11.5 years ago by
Deniz
▴ 210
23
votes
16
replies
32k
views
11 follow
Any tools converting Genbank format to GFF3 format?
genbank
gff
updated 9 months ago by
Matteo Schiavinato
★ 3.6k • written 8.2 years ago by
biolab
★ 1.4k
50
votes
18
replies
32k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq
macs
ChIP-Seq
peaks
updated 7 weeks ago by
e.r.zakiev
▴ 50 • written 6.8 years ago by
igor
13k
62
votes
16
replies
32k
views
18 follow
Job:
Bioinformatics Jobs You Can Do From Home?
python
education
updated 3 months ago by
Ram
39k • written 12.7 years ago by
Ivana
▴ 290
27
votes
16
replies
32k
views
16 follow
How Do I Convert Fa Files To Bed Format?
fasta
bed
updated 11 weeks ago by
shelkmike
▴ 920 • written 11.5 years ago by
Keziah
▴ 70
5
votes
3
replies
32k
views
Best method/package for Gene Set Enrichment Analysis in R?
GSEA
Bioconductor
GO
updated 9 months ago by
Ram
39k • written 7.5 years ago by
Juan Cordero
▴ 120
21
votes
3
replies
32k
views
Forum:
Did You Know That Researchgate Is Spamming Your Colleagues (Perhaps Without Your Explicit Consent)?
researchgate
updated 3 months ago by
Ram
39k • written 10.3 years ago by
Obi Griffith
20k
24
votes
18
replies
32k
views
11 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 8 weeks ago by
Pierre Lindenbaum
154k • written 8.9 years ago by
onter
▴ 160
71
votes
17
replies
32k
views
14 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 4 months ago by
Ming Tommy Tang
★ 2.9k • written 9.1 years ago by
M K
▴ 600
29
votes
6
replies
32k
views
6 follow
Snp Quality In Vcf File
vcf
mpileup
snp
dbsnp
updated 8 months ago by
Kermit
▴ 80 • written 11.9 years ago by
Tiffani
▴ 150
65
votes
17
replies
32k
views
12 follow
Transform a GTF file into a data frame in R
R
RNA-Seq
GTF
updated 3 months ago by
Ram
39k • written 5.7 years ago by
biomagician
▴ 360
67
votes
15
replies
32k
views
14 follow
Rna-Seq Pipeline
pipeline
next-gen-sequencing
rna
rna-seq
updated 18 days ago by
Ram
39k • written 13.0 years ago by
brentp
24k
1,000 results • Page
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Recent Votes
Answer: calculate p value and associated z score for snp-gene pair
Answer: calculate p value and associated z score for snp-gene pair
Answer: I need help with a blast command, please help
Answer: I need help with a blast command, please help
Answer: NCBI API, Perl
Get a list of genes associated with a drug in 1 min
Answer: Getting species names and taxa id from assembly accession number
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Recent Replies
Comment: calculate p value and associated z score for snp-gene pair
by
rheab1230
▴ 140
Thank you so much for this. Yes, in this case I get all the SNPs. I also have one more question: SNP gene beta t-stat p-value FDR …
Comment: Is RNA-Seq well suited for studying pseudogenes and lncRNA?
by
rpolicastro
12k
lncRNAs are usually fine to include in downstream analysis since they are generally not selected against in most RNA-seq library prep proto…
Comment: I need help with a blast command, please help
by
neto.pvp
• 0
Thank you very much!! I'm new to this subject and I believe your answer gave me a great idea of where to go next, thanks again!!
Answer: NCBI API, Perl
by
GenoMax
129k
You are likely best served by using `NCBI datasets` ([**LINK**][1]) or `EntrezDirect` ([**LINK**][2]) command line tools. If you want to …
Comment: Obtain a --gene-trans-map file after rnaSPAdes
by
GenoMax
129k
You could try to create one: https://groups.google.com/g/trinityrnaseq-users/c/qPbWnLl4iY0 While this is from an unrelated software the so…
Comment: CNNScoreVariants Error
by
Pierre Lindenbaum
154k
that is another question
Comment: Difference between USCS exon coordinates and ensembl
by
amy__
▴ 50
Hi @atpoint, I went to http://genome.ucsc.edu/cgi-bin/hgTables and did: 1. ![enter image description here][1] then: 2. ![enter image…
Comment: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex
by
Kermit
▴ 80
See also: https://www.biostars.org/p/9535550/#9536086
Answer: Getting species names and taxa id from assembly accession number
by
MirianT_NCBI
▴ 590
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder
by
GenoMax
129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output
by
rpolicastro
12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl
by
ATpoint
72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin
by
sativus
• 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis
by
nux
▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
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