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1,000 results • Page
3 of 20
Sort: Views
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Views
Votes
Replies
40
votes
7
replies
63k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r
rna
heatmap
clustering
gene
updated 15 months ago by
Ram
40k • written 11.9 years ago by
Kanne
▴ 450
25
votes
5
replies
61k
views
7 follow
Rpkm Calculation For Genes
rpkm
rna-seq
updated 10.9 years ago by
JC
13k • written 10.9 years ago by
siddharth.sethi5
▴ 270
36
votes
14
replies
61k
views
9 follow
What Is The Difference Between Hg18 And Hg19?
genome
hg
hg
updated 11.6 years ago by
Jorge Amigo
14k • written 11.6 years ago by
Sara
▴ 170
156
votes
24
replies
60k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 3 months ago by
Ram
40k • written 10.6 years ago by
Nicolas Rosewick
10k
328
votes
54
replies
60k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome
visualization
updated 12 months ago by
Kevin Blighe
86k • written 13.5 years ago by
brentp
24k
102
votes
30
replies
60k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 3 months ago by
Ram
40k • written 13.6 years ago by
Biostar User
★ 1.0k
62
votes
22
replies
60k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf
bed
updated 9 months ago by
leshaker
• 0 • written 10.9 years ago by
biorepine
★ 1.5k
149
votes
35
replies
60k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 7 months ago by
Ram
40k • written 10.8 years ago by
vijay
★ 1.6k
91
votes
25
replies
60k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks
selection
software
updated 12 months ago by
Michael
53k • written 12.6 years ago by
Jarretinha
3.4k
27
votes
21
replies
59k
views
21 follow
Public Electronic Health Records Database
database
updated 2.0 years ago by
Ram
40k • written 10.4 years ago by
Abhi
★ 1.6k
134
votes
33
replies
59k
views
19 follow
VCF files: Change Chromosome Notation
vcf
next-gen
sequence
updated 11 months ago by
Ram
40k • written 9.4 years ago by
Quak
▴ 480
53
votes
20
replies
59k
views
14 follow
Bam Header Edit
bam
updated 13 months ago by
Ram
40k • written 11.3 years ago by
Ashutosh Pandey
12k
53
votes
8
replies
59k
views
8 follow
What Is A Good Threshold For Log2 Fold Change?
microarray
gene
updated 8.6 years ago by
Biostar
20 • written 12.5 years ago by
Some
▴ 90
100
votes
6
replies
59k
views
6 follow
Insert Size And Fragment Size ?
23 months ago by
Nicolas Rosewick
10k
39
votes
20
replies
59k
views
8 follow
How to convert to .SRA files to .FQ (FASTQ)
fastq
FASTQ
sra
RNA-Seq
SRAA
updated 19 months ago by
aimanbarki
▴ 20 • written 9.1 years ago by
Veli Kaan Aydin
▴ 50
2
votes
10
replies
59k
views
R: remove rows by a list of rownames
R
updated 17 months ago by
Ram
40k • written 8.7 years ago by
silvi_free88
▴ 50
17
votes
6
replies
59k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
sequence
blast
updated 3.1 years ago by
yasopi9568
• 0 • written 13.6 years ago by
Zhaorong
★ 1.4k
90
votes
44
replies
59k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 17 months ago by
Ram
40k • written 12.4 years ago by
Ryan D
★ 3.4k
37
votes
5
replies
58k
views
Idenity, e value or bitscore ?
blast
annotation
updated 4.3 years ago by
alslonik
▴ 300 • written 7.4 years ago by
Leo
▴ 60
1
vote
6
replies
57k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 6 months ago by
Ram
40k • written 6.7 years ago by
IOM
• 0
19
votes
2
replies
57k
views
Keeping pheatmap colour range the same for different data sets
R
RNA-Seq
pheatmap
updated 7.4 years ago by
Selenocysteine
▴ 620 • written 7.4 years ago by
as9309
▴ 60
93
votes
19
replies
57k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 3 months ago by
Ram
40k • written 13.0 years ago by
Niek De Klein
★ 2.6k
7
votes
3
replies
57k
views
what is the difference between single end and paired end in sequencing
RNA-Seq
updated 23 months ago by
Ram
40k • written 9.3 years ago by
M K
▴ 620
164
votes
70
replies
57k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen
sequencing
fastq
parsing
updated 11.7 years ago by
Ric
▴ 430 • written 12.2 years ago by
Panos
★ 1.8k
1
vote
3
replies
57k
views
Error in loading R package "GO.db" in installing WGCNA R package
R
updated 16 months ago by
Ram
40k • written 8.6 years ago by
zaynabmousavian
▴ 10
76
votes
24
replies
57k
views
16 follow
How To Sort Bed Format File
bed
updated 11 months ago by
Pierre Lindenbaum
157k • written 10.6 years ago by
lyz10302012
▴ 450
131
votes
22
replies
56k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 3 months ago by
Kevin Blighe
86k • written 5.8 years ago by
Mike
★ 1.9k
85
votes
2
replies
56k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 6 months ago by
Ram
40k • written 10.2 years ago by
Eric Normandeau
11k
15
votes
5
replies
55k
views
R Help: For Loop Over Range Of Number And Calculate Average Using An If Statement
r
updated 7.7 years ago by
Biostar
20 • written 9.6 years ago by
714
▴ 110
62
votes
24
replies
55k
views
20 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 20 months ago by
Ram
40k • written 10.7 years ago by
rehma.ar
▴ 290
12
votes
7
replies
55k
views
Use Python To List Filename With Specific Extensions.
python
updated 12.3 years ago by
Giovanni M Dall'Olio
28k • written 12.3 years ago by
Bioscientist
★ 1.7k
50
votes
5
replies
54k
views
6 follow
Subsampling Bam File With Samtools
samtools
bam
updated 24 months ago by
eidriangm
▴ 50 • written 10.2 years ago by
madbessoul
▴ 250
72
votes
18
replies
54k
views
13 follow
Extracting Multiple Fasta Sequences At A Time From A File Containing Many Sequences
fasta
sequence
parsing
perl
updated 13.0 years ago by
Peter
6.0k • written 13.0 years ago by
Sarah
▴ 110
12
votes
13
replies
54k
views
pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R
RNA-Seq
pheatmap
arg10
updated 2.7 years ago by
henry-keen
▴ 40 • written 3.2 years ago by
camillab.
▴ 130
30
votes
8
replies
54k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma
microarray
topTable
R
updated 14 months ago by
Ram
40k • written 9.4 years ago by
komal.rathi
★ 4.1k
38
votes
41
replies
54k
views
9 follow
Volcano Plot from DEseq2
R
written 5.9 years ago by
1769mkc
★ 1.1k
47
votes
10
replies
53k
views
7 follow
RNA-seq: Explain STAR quantMode geneCounts values
RNA-Seq
STAR
Differential expression
updated 5.5 years ago by
Tao
▴ 520 • written 6.9 years ago by
williantafsilva
▴ 360
28
votes
22
replies
53k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r
genomics
entrez
updated 12 weeks ago by
cwang3444
• 0 • written 10.4 years ago by
grosy
▴ 90
0
votes
6
replies
53k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
R
heatmap
error
updated 2.3 years ago by
Abdul Aziz
• 0 • written 4.5 years ago by
luzglongoria
▴ 50
61
votes
12
replies
53k
views
7 follow
Recommended cutoff for FDR - 0.05 or 0.1
RNA-Seq
R
updated 2.5 years ago by
George
• 0 • written 7.1 years ago by
aggregatibacter
▴ 180
84
votes
12
replies
53k
views
9 follow
What are chimeric reads?
sequence
updated 20 months ago by
Ram
40k • written 8.9 years ago by
zhangz.cs
▴ 290
42
votes
26
replies
53k
views
11 follow
How To Interpret A T-Test Output Produced By R
statistics
updated 10.2 years ago by
Biostar
20 • written 11.2 years ago by
Panos
★ 1.8k
16
votes
30
replies
53k
views
9 follow
Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
dna
sequence
retrieval
perl
bioperl
updated 12.6 years ago by
Palu
▴ 290 • written 12.6 years ago by
Samad
▴ 90
77
votes
27
replies
53k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 13 months ago by
Johan Zicola
▴ 70 • written 9.8 years ago by
Ram
▴ 180
146
votes
34
replies
53k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 7 months ago by
Ram
40k • written 10.4 years ago by
Cyriac Kandoth
6.0k
57
votes
22
replies
53k
views
14 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam
mapping
updated 14 months ago by
Alex Reynolds
35k • written 10.6 years ago by
Jordan
★ 1.3k
95
votes
5
replies
53k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools
clipped-reads
soft-clip
bam
hard-clip
updated 21 months ago by
Ram
40k • written 9.1 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
10
votes
8
replies
52k
views
geom_bar plot with several variables
R
ggplot2
updated 4.2 years ago by
gpushpaganesan
• 0 • written 4.6 years ago by
jordi.planells
▴ 450
80
votes
27
replies
52k
views
23 follow
Renaming Entries In A Fasta File
fasta
updated 7.4 years ago by
noirot.celine
▴ 50 • written 11.0 years ago by
thiago84naka
▴ 130
1.2k
votes
206
replies
52k
views
108 follow
Forum:
What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 3 months ago by
Raony Guimarães
★ 1.2k • written 12.5 years ago by
Jeremy Leipzig
21k
1,000 results • Page
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Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
ATpoint
76k
Generally these genes are highly expressed, so there would be some sort of a power bias. How do you do the DE analysis? Any cutoffs on mini…
Answer: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2
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Answer: how to identify uniq genes between two gff files.
by
Juke34
8.2k
You can run `agat_sp_compare_two_annotations.pl` from [AGAT][1], you should get the information you are looking for. This method allow to c…
Comment: How to find out what adapters to remove after FastQC of RNAseq data?
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Thank you for the fast help, I have the BBMap suite installed anyways and will try it out :)
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by
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thanks a lot! can't believe that is so simple
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
yes got it, thank you very much.
Comment: SCENIC-openloom not working
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kyriakds
• 0
Hello, Did you find a solution in the end?
Comment: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
Vijith
▴ 30
@swbarnes2, thanks for the response, by the way, can you tell me why/ how this happens during the sequencing process, and if it could negat…
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
> can you explain this ?? yes. you should use options like `-u` . > Write original A entry once if any overlaps found in B. In other word…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
Pierre Lindenbaum
157k
so validate the answer to close the question please (Green tick on the left).
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
hi Pierre Linderbaum, after extracting genes, I have 5846 genes in afile.bed and 4456 genes in bfile.bed , while using bedtools intersec…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
nikhil
▴ 10
thank you, bcftools isec is working well.
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
please, comment or validate the answers to your previous questions: https://www.biostars.org/p/9573151/#9573158 ; https://www.biostars.org/…
Answer: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
extract genes (e.g: awk '($3=="gene") {printf("%s\t%d\t%s\n",$1;int($4)-1,$5);}' ) from both files n sort, and use bedtools intersect with…
Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
swbarnes2
13k
G is the letter you get if there is no fluorescence. 75% of your reads have a lot of G. I don't think this run worked.
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