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1,000 results • Page 6 of 20
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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 ▴ 70 • written 13.1 years ago by 2.8k
18
votes
21
replies
43k
views
11 follow
R org.Hs.eg.db matching ensembl gene ids with gene symbol
bioconductor R
updated 2.6 years ago by ▴ 10 • written 8.2 years ago by ▴ 330
48
votes
33
replies
43k
views
16 follow
Extract A Group Of Fasta Sequences From A File
fasta python perl biopython bioperl
updated 2.4 years ago by 43k • written 13.8 years ago by ▴ 60
2
votes
4
replies
43k
views
python 3.8 'No module named pip'
rna-seq
updated 2.9 years ago by ▴ 10 • written 3.8 years ago by • 0
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 11k • written 11.3 years ago by ▴ 810
15
votes
12
replies
43k
views
8 follow
Intall local BLAST in Ubuntu
blast local system requirement Ubuntu
updated 3.9 years ago by ▴ 460 • written 6.7 years ago by ▴ 30
39
votes
17
replies
43k
views
13 follow
Extract Cds Fastas From A Gff Annotation + Reference Sequence
gff CDS
updated 14 months ago by 43k • written 11.9 years ago by ▴ 730
40
votes
4
replies
42k
views
What Is Snp Calling?
snp next-gen sequencing snp
updated 13.3 years ago by • 0 • written 14.0 years ago by 28k
81
votes
21
replies
42k
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 ▴ 210 • written 10.2 years ago by ▴ 750
10
votes
16
replies
42k
views
6 follow
Beginner in Python- need in assistance translating DNA into protein sequence
python
updated 3.2 years ago by • 0 • written 7.4 years ago by ▴ 10
20
votes
4
replies
42k
views
what does a log 2-fold change values of mean ?
motif microarray gene genesequencing sequencing
5.5 years ago by a4appy23 ▴ 50
45
votes
7
replies
42k
views
9 follow
Any Good Bam And Sam Viewer?
viewer sam bam
updated 2.3 years ago by 43k • written 12.6 years ago by ▴ 160
18
votes
6
replies
42k
views
How can I convert -log10 (p-value) to p-value?
p-value
updated 18 months ago by ★ 1.2k • written 5.3 years ago by ▴ 80
26
votes
13
replies
42k
views
7 follow
what is the difference between GRCh37 and hg19 ?
RNA-Seq Assembly genome alignment
updated 2.1 years ago by 43k • written 9.4 years ago by ▴ 960
40
votes
13
replies
42k
views
8 follow
Difference between FC and LogFC
r microarray
updated 2.3 years ago by • 0 • written 6.0 years ago by ▴ 120
60
votes
12
replies
42k
views
10 follow
Get chromosome sizes from fasta file
genome ucsc
updated 18 months ago by • 0 • written 8.3 years ago by ▴ 710
23
votes
4
replies
42k
views
What is the difference between GTF AND GFF format
RNA-Seq
updated 10.0 years ago by ▴ 160 • written 10.0 years ago by ▴ 230
14
votes
6
replies
42k
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 20 months ago by ▴ 220 • written 10.7 years ago by ▴ 20
42
votes
21
replies
42k
views
11 follow
Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elements
unix list intersect
updated 2.4 years ago by 43k • written 11.2 years ago by ▴ 620
46
votes
9
replies
42k
views
9 follow
How To Convert Centimorgan To Base Pair
genetics distance
updated 19 months ago by 43k • written 12.3 years ago by ▴ 90
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 9 days ago by 43k • written 6.7 years ago by ★ 1.3k
16
votes
5
replies
42k
views
Understand Samtools View Output
samtools
updated 2.5 years ago by 43k • written 12.8 years ago by ▴ 520
64
votes
24
replies
42k
views
12 follow
How to extract unique mapped results from Bowtie2 bam results?
alignment
updated 16 months ago by 43k • written 9.9 years ago by ▴ 170
33
votes
4
replies
42k
views
What read lengths are produced by modern Illumina sequencers?
read-length dna illumina
updated 2.3 years ago by 43k • written 9.9 years ago by ▴ 320
29
votes
5
replies
41k
views
What Does Up-Regulated And Down-Regulated Mean？
updated 2.3 years ago by • 0 • written 12.0 years ago by ▴ 100
53
votes
21
replies
41k
views
12 follow
How To Filter Multi Fasta By Length??
awk
updated 5.7 years ago by 43k • written 10.7 years ago by ★ 1.2k
4
votes
4
replies
41k
views
How to convert a URL into a DOI programmatically
pubmed doi url
written 7.6 years ago by ▴ 100
13
votes
8
replies
41k
views
6 follow
Bowtie2 Ubuntu Installation
ubuntu bowtie
updated 3.3 years ago by • 0 • written 11.7 years ago by ▴ 30
50
votes
21
replies
41k
views
11 follow
How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
rpkm rna-seq cutoff fpkm
updated 2.5 years ago by 43k • written 11.3 years ago by ★ 1.5k
18
votes
5
replies
41k
views
R - pheatmap - changing column order
pheatmap heatmap R
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 60
33
votes
12
replies
41k
views
8 follow
How To Find Paralogs Using Blast
homology blast
updated 12.1 years ago by 16k • written 12.7 years ago by ▴ 380
26
votes
19
replies
41k
views
7 follow
Fasta File Vs Fa File
fasta sequence
updated 12.8 years ago by 24k • written 12.8 years ago by ▴ 520
206
votes
58
replies
41k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
6
votes
7
replies
41k
views
6 follow
Bowtie Building Index Issue
bowtie bowtie2 genome
updated 11.9 years ago by 100k • written 11.9 years ago by ▴ 40
82
votes
13
replies
41k
views
7 follow
Ti/Tv Ratio Confirms Snp Discovery. Is This A General Rule?
snp snp
updated 3.7 years ago by 20 • written 13.3 years ago by ▴ 210
42
votes
4
replies
41k
views
What Control For Chip-Seq: Input, Igg Or Untagged Strain?
chip-seq
updated 12.3 years ago by ★ 4.2k • written 12.3 years ago by ▴ 180
17
votes
7
replies
41k
views
6 follow
Calculating Genomic Inflation Factor
gwas plink
updated 7.2 years ago by ▴ 670 • written 12.0 years ago by ▴ 30
27
votes
12
replies
41k
views
7 follow
Log2 Ratio or Log2 Fold Change - terminology confusion and which one should I use?
genome
updated 21 months ago by ▴ 30 • written 7.5 years ago by ▴ 160
6
votes
11
replies
40k
views
Finding The Mean Of Values In A Single Column
r
updated 10.5 years ago by 54k • written 10.5 years ago by ▴ 110
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 5 months ago by 161k • written 14.0 years ago by ▴ 660
49
votes
23
replies
40k
views
13 follow
Concatenating fastq.gz files across lanes
RNA-Seq
updated 2.2 years ago by ▴ 10 • written 5.9 years ago by ▴ 40
13
votes
10
replies
40k
views
7 follow
How To Uncompress The 1000 Genome Vcf.Gz File
updated 2.6 years ago by • 0 • written 11.5 years ago by ▴ 390
17
votes
25
replies
40k
views
7 follow
Remove columns and rows which have only NAs without deleting all the data
missing data R correlation SNPs
updated 5.4 years ago by • 0 • written 6.8 years ago by • 0
35
votes
11
replies
40k
views
9 follow
Is It Possible To Get Fragment Length, Read Length And Number Of Fragments From A Bam/Sam File
bam next-gen
updated 7.3 years ago by ▴ 130 • written 11.2 years ago by ▴ 630
36
votes
8
replies
40k
views
9 follow
Difference Between "Mate Pair" And "Pair-End"
paired-end ngs library
updated 16 months ago by ★ 3.8k • written 10.8 years ago by ▴ 150
28
votes
10
replies
40k
views
6 follow
Extract subset of samples from multigenome vcf file
vcf
8.1 years ago by MAPK ★ 2.1k
58
votes
25
replies
40k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 13 months ago by 43k • written 7.7 years ago by ★ 9.4k
15
votes
2
replies
40k
views
what is difference between sequence adapter and PCR primer?
adapter pcr
updated 15 months ago by 43k • written 8.9 years ago by ▴ 120
160
votes
19
replies
40k
views
16 follow
Why Does Rna-Seq Read Count Fit Poisson Distribution?
rna-seq modeling
updated 2.3 years ago by 43k • written 10.5 years ago by ▴ 730
28
votes
14
replies
40k
views
8 follow
Running and Analyzing fastqc on multiple fastq files
next-gen RNA-Seq genome
updated 14 months ago by 43k • written 9.0 years ago by ▴ 220
1,000 results • Page 6 of 20
Recent Votes
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
Converting between Ensembl Versions
Comment: what is the purpose of indexing the reference genome (Kallisto)
Answer: what is the purpose of indexing the reference genome (Kallisto)
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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Recent Replies
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question by starswillfade ▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question by starswillfade ▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt by GenoMax 141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto) by i.sudbery 19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by benformatics 3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto) by dsull ★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by Jalil Sharif ▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis by The_PyPanda ▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads by Antonio R. Franco ★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
Comment: PCA plot by ATpoint 82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt by Joe 21k
If you have the accession numbers can you not use something like `eutils`?
Comment: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
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