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1,000 results • Page 3 of 20
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45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
10
votes
5
replies
36k
views
How to compare 2 VCF files
vcf SNP
updated 5 months ago by 41k • written 9.6 years ago by ▴ 100
69
votes
17
replies
35k
views
12 follow
Transform a GTF file into a data frame in R
R RNA-Seq GTF
updated 9 months ago by 41k • written 6.2 years ago by ▴ 410
10
votes
6
replies
35k
views
generating genome indexes with STAR
RNA-Seq STAR
updated 4 months ago by ★ 3.3k • written 7.5 years ago by ▴ 50
74
votes
15
replies
35k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 23 days ago by 41k • written 13.6 years ago by 158k
27
votes
21
replies
35k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 7 weeks ago by ▴ 50 • written 9.4 years ago by ▴ 170
50
votes
18
replies
35k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq macs ChIP-Seq peaks
updated 5 months ago by 41k • written 7.3 years ago by 13k
78
votes
21
replies
35k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 20 days ago by • 0 • written 9.6 years ago by ▴ 650
132
votes
123
replies
35k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 months ago by ★ 1.1k • written 5.1 years ago by 86k
23
votes
4
replies
35k
views
bcftools compressing and indexing vcf files
sequence bcftools vcf index
updated 4 weeks ago by 136k • written 5.2 years ago by ▴ 270
118
votes
26
replies
35k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 9 months ago by ▴ 170 • written 8.6 years ago by ▴ 610
6
votes
25
replies
34k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 6 months ago by • 0 • written 5.7 years ago by ▴ 130
62
votes
17
replies
34k
views
7 follow
how to remove multiallelic from VCF
SNP
updated 10 months ago by 41k • written 8.6 years ago by ▴ 530
28
votes
16
replies
34k
views
16 follow
How Do I Convert Fa Files To Bed Format?
fasta bed
updated 8 months ago by ★ 1.1k • written 12.0 years ago by ▴ 70
31
votes
10
replies
34k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq ensembl
updated 4 months ago by 41k • written 9.4 years ago by ▴ 520
40
votes
10
replies
34k
views
7 follow
Can'T Locate Vcf.Pm Vcftools
vcftools vcf
updated 10 months ago by 41k • written 12.0 years ago by ▴ 210
13
votes
3
replies
34k
views
Drawing venn diagram in R
ChIP-Seq venn-diagram
updated 8 months ago by 41k • written 8.6 years ago by ▴ 470
7
votes
6
replies
33k
views
Can the code of a R package be changed? How?
R
updated 11 months ago by 41k • written 8.5 years ago by ★ 5.1k
62
votes
16
replies
33k
views
18 follow
Job: Bioinformatics Jobs You Can Do From Home?
python education
updated 9 months ago by 41k • written 13.2 years ago by ▴ 290
60
votes
17
replies
33k
views
16 follow
Scientific Names In Blast Output And Databases
blast blast+
updated 11 months ago by 41k • written 10.4 years ago by ★ 2.1k
197
votes
27
replies
33k
views
20 follow
Forum: Bioinformatics Cartoon
bioinformatics
updated 4 months ago by 41k • written 11.9 years ago by ★ 2.3k
13
votes
12
replies
33k
views
Estimating Insert Size From Paired End Data.
picard alignment paired-end
updated 10 weeks ago by 41k • written 9.8 years ago by 12k
21
votes
8
replies
33k
views
8 follow
Merging/Concatenating Vcf Files
vcftools snp indel
updated 3 months ago by ▴ 330 • written 11.3 years ago by ▴ 830
67
votes
15
replies
32k
views
14 follow
Rna-Seq Pipeline
pipeline next-gen-sequencing rna rna-seq
updated 6 months ago by 41k • written 13.6 years ago by 24k
60
votes
3
replies
32k
views
Paired-end reads - what is what?
RNA-Seq
updated 11 months ago by 41k • written 8.5 years ago by ▴ 220
21
votes
3
replies
32k
views
Forum: Did You Know That Researchgate Is Spamming Your Colleagues (Perhaps Without Your Explicit Consent)?
researchgate
updated 9 months ago by 41k • written 10.8 years ago by 20k
251
votes
36
replies
32k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 8 months ago by 41k • written 13.6 years ago by 158k
37
votes
11
replies
32k
views
8 follow
Wright'S Fst And Weir & Cockerham'S Fst Estimator - Simple Explanation Of The Difference
fst population-genetics
updated 11 months ago by 41k • written 10.4 years ago by ▴ 450
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 8 months ago by 41k • written 7.3 years ago by 26k
43
votes
21
replies
32k
views
16 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 10 months ago by 41k • written 10.2 years ago by ★ 5.2k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 9 months ago by 41k • written 11.2 years ago by 99k
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 weeks ago by ▴ 50 • written 3.3 years ago by ▴ 160
90
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 9 months ago by 41k • written 10.1 years ago by 20k
27
votes
14
replies
31k
views
samtools (conversion from .sam to .bam) and sorting of .bam file
alignment genome next-gen-sequencing
updated 11 months ago by 41k • written 8.5 years ago by ▴ 220
117
votes
59
replies
31k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware next-gen
updated 10 months ago by 41k • written 8.6 years ago by ▴ 30
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 weeks ago by 41k • written 10.1 years ago by ★ 7.8k
20
votes
9
replies
31k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart r bioconductor
updated 7 months ago by 86k • written 11.4 years ago by ▴ 120
48
votes
18
replies
31k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 23 days ago by 41k • written 13.6 years ago by ★ 1.6k
15
votes
8
replies
31k
views
8 follow
How to read vcf file in python?
vcf reader python
updated 9 months ago by ▴ 70 • written 3.9 years ago by ▴ 20
130
votes
44
replies
31k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 9 months ago by 41k • written 7.2 years ago by ★ 1.0k
19
votes
10
replies
31k
views
6 follow
read depth using samtools
depth samtools
updated 11 weeks ago by • 0 • written 4.9 years ago by ▴ 30
26
votes
35
replies
31k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 10 months ago by ▴ 10 • written 9.7 years ago by ★ 4.1k
10
votes
10
replies
31k
views
7 follow
How To Download .Gbk Files From Ncbi Website
ncbi genbank
updated 8 months ago by 41k • written 12.0 years ago by • 0
185
votes
45
replies
31k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline general
updated 7 weeks ago by 41k • written 13.8 years ago by 28k
36
votes
11
replies
31k
views
6 follow
Sjdboverhang Option In Star
updated 5 months ago by ▴ 80 • written 9.8 years ago by ★ 3.1k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 26 days ago by 41k • written 13.7 years ago by 158k
8
votes
6
replies
30k
views
6 follow
Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Files?
hg19 ucsc
updated 11 months ago by 41k • written 10.4 years ago by ▴ 100
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 4 months ago by • 0 • written 7.7 years ago by 20k
37
votes
16
replies
30k
views
14 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 11 weeks ago by ★ 1.2k • written 4.8 years ago by ▴ 60
7
votes
10
replies
30k
views
6 follow
Converting Sam To Bam
bam sam
updated 11 months ago by 41k • written 11.9 years ago by ▴ 190
1,000 results • Page 3 of 20
Recent Votes
C: PCA vs ICA prior to t-SNE or UMAP
C: PCA vs ICA prior to t-SNE or UMAP
Answer: Calculate GC content for entire chromosome
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV by awhale01 • 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
Yes at 5%.
Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k
Has phiX been spiked in to increase nucleotide diversity.
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