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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
35
votes
9
replies
63k
views
8 follow
Minor allele frequency calculation
SNP
next-gen
updated 8 months ago by
Ram
37k • written 8.2 years ago by
Tark
▴ 50
40
votes
7
replies
62k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r
rna
heatmap
clustering
gene
updated 7 months ago by
Ram
37k • written 11.2 years ago by
Kanne
▴ 450
51
votes
15
replies
62k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization
software
updated 9 months ago by
Ram
37k • written 11.6 years ago by
Michael Petronio
▴ 70
53
votes
4
replies
59k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence
next-gen-sequencing
updated 3 months ago by
Ram
37k • written 8.2 years ago by
mangfu100
▴ 780
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
tool
updated 7 months ago by
Ram
37k • written 12.9 years ago by
Biostar User
★ 1.0k
152
votes
24
replies
58k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing
tools
rna-seq
alternative-splicing
updated 6 months ago by
Ram
37k • written 9.9 years ago by
Nicolas Rosewick
10k
2
votes
10
replies
58k
views
R: remove rows by a list of rownames
R
updated 9 months ago by
Ram
37k • written 8.0 years ago by
silvi_free88
▴ 50
146
votes
35
replies
57k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
Tutorial
next-gen
updated 8 months ago by
Bramadi Arya
• 0 • written 10.2 years ago by
vijay
★ 1.6k
361
votes
57
replies
57k
views
43 follow
Forum:
Recommend Your Favorite Bioinformatics Books
books
education
updated 4 months ago by
Kevin Blighe
84k • written 12.9 years ago by
Istvan Albert
96k
91
votes
25
replies
57k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks
selection
software
updated 4 months ago by
Michael Dondrup
52k • written 11.9 years ago by
Jarretinha
3.4k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 9 months ago by
Ram
37k • written 11.8 years ago by
Ryan D
★ 3.4k
328
votes
54
replies
56k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome
visualization
updated 4 months ago by
Kevin Blighe
84k • written 12.9 years ago by
brentp
24k
11
votes
9
replies
56k
views
7 follow
combining fasta files
windows
fasta
notepad
updated 10 weeks ago by
Devarakonda
• 0 • written 8.0 years ago by
vigneshprbh37
▴ 30
87
votes
18
replies
55k
views
12 follow
Sequence length from Fasta
fasta
updated 5 weeks ago by
Ram
37k • written 8.2 years ago by
bongbang
▴ 80
93
votes
19
replies
55k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree
tool
phylogenetics
viewer
updated 8 months ago by
Theo
▴ 20 • written 12.4 years ago by
Niek De Klein
★ 2.6k
49
votes
20
replies
55k
views
14 follow
Bam Header Edit
bam
updated 5 months ago by
Ram
37k • written 10.7 years ago by
Ashutosh Pandey
12k
24
votes
10
replies
55k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
Tutorial
error
software
R
updated 8 months ago by
Chih
• 0 • written 22 months ago by
Nitin Narwade
★ 1.3k
38
votes
20
replies
54k
views
8 follow
How to convert to .SRA files to .FQ (FASTQ)
fastq
FASTQ
sra
RNA-Seq
SRAA
updated 11 months ago by
aimanbarki
▴ 20 • written 8.5 years ago by
Veli Kaan Aydin
▴ 50
62
votes
22
replies
54k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf
bed
updated 7 weeks ago by
leshaker
• 0 • written 10.2 years ago by
biorepine
★ 1.5k
78
votes
2
replies
53k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
tutorial
Tutorial
written 9.6 years ago by
Eric Normandeau
11k
45
votes
14
replies
52k
views
10 follow
Tutorial:
Using R in Conda
R
Tutorial
updated 12 weeks ago by
Ann
▴ 20 • written 2.5 years ago by
rohitsatyam102
▴ 690
74
votes
24
replies
51k
views
16 follow
How To Sort Bed Format File
bed
updated 3 months ago by
Pierre Lindenbaum
152k • written 9.9 years ago by
lyz10302012
▴ 430
126
votes
33
replies
51k
views
19 follow
VCF files: Change Chromosome Notation
vcf
next-gen
sequence
updated 3 months ago by
Ram
37k • written 8.8 years ago by
Quak
▴ 480
143
votes
34
replies
51k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation
maf
tcga
cancer
music
Tutorial
updated 8 months ago by
Ram
37k • written 9.8 years ago by
Cyriac Kandoth
5.8k
27
votes
8
replies
50k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma
microarray
topTable
R
updated 6 months ago by
Ram
37k • written 8.7 years ago by
komal.rathi
★ 4.0k
75
votes
22
replies
49k
views
17 follow
How To Download All Sra Samples At Once ?
geo
download
sra
updated 10 months ago by
solomoncharles77
▴ 90 • written 8.9 years ago by
biorepine
★ 1.5k
77
votes
27
replies
48k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 5 months ago by
Johan Zicola
▴ 70 • written 9.1 years ago by
Ram
▴ 180
1.2k
votes
205
replies
47k
views
107 follow
Forum:
What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 11 days ago by
jena
▴ 240 • written 11.8 years ago by
Jeremy Leipzig
21k
87
votes
37
replies
47k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 10 months ago by
Ram
37k • written 9.5 years ago by
Hunter
▴ 110
45
votes
3
replies
47k
views
Gwas Vs. Qtl Mapping?
gwas
mapping
updated 7 months ago by
Ram
37k • written 10.6 years ago by
Justin
▴ 460
54
votes
22
replies
47k
views
14 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam
mapping
updated 6 months ago by
Alex Reynolds
34k • written 9.9 years ago by
Jordan
★ 1.2k
57
votes
15
replies
46k
views
11 follow
Filtering Vcf File
vcftools
vcf
snp
indel
updated 11 months ago by
Ram
37k • written 10.4 years ago by
bioinfo
▴ 830
65
votes
17
replies
46k
views
15 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
tools
updated 4 weeks ago by
Ram
37k • written 10.0 years ago by
14134125465346445
★ 3.6k
42
votes
11
replies
45k
views
10 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 5 months ago by
Ram
37k • written 7.1 years ago by
nash.claire
▴ 460
112
votes
24
replies
44k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp
samtools
alignment
next-gen
sequencing
updated 5 months ago by
Ram
37k • written 11.7 years ago by
Matthieu
▴ 480
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 8 months ago by
Ram
37k • written 7.9 years ago by
MAPK
★ 2.0k
32
votes
19
replies
43k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
convert
updated 4 weeks ago by
Ram
37k • written 9.7 years ago by
hicsuntdrac0nis
▴ 240
77
votes
18
replies
43k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 6 months ago by
Dan
• 0 • written 12.7 years ago by
Science_Robot
★ 1.1k
48
votes
4
replies
42k
views
How To Convert The Bed File To Ped File
bed
ped
updated 4 months ago by
sonsunjirachote
• 0 • written 12.4 years ago by
Austinlew
▴ 310
31
votes
7
replies
42k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq
deseq2
tpm
updated 6 months ago by
Ram
37k • written 7.9 years ago by
Tom Harrop
▴ 170
39
votes
16
replies
42k
views
10 follow
How to split paired end SRA file into 2 correct fastq files
next-gen
sra
fastq
updated 11 months ago by
Alejandro Miguel
▴ 10 • written 6.2 years ago by
thustar
▴ 120
142
votes
68
replies
42k
views
18 follow
Tutorial:
Network plot from expression data in R using igraph
R
Tutorial
microarray
RNA-Seq
network
updated 7 months ago by
Guido
• 0 • written 5.2 years ago by
Kevin Blighe
84k
32
votes
10
replies
41k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat
illumina
strand
updated 3 months ago by
Ram
37k • written 9.9 years ago by
Nicolas Rosewick
10k
116
votes
74
replies
41k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 12 weeks ago by
GenoMax
125k • written 12.1 years ago by
Casbon
★ 3.2k
31
votes
11
replies
41k
views
9 follow
How To Sort Sam File
samtools
sam
updated 19 days ago by
Ram
37k • written 8.9 years ago by
Chen Sun
★ 1.1k
51
votes
19
replies
41k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq
rna-seq
bigwig
visualization
ucsc
tutorial
Tutorial
updated 6 months ago by
Ram
37k • written 10.8 years ago by
Sukhi Singh
11k
292
votes
27
replies
41k
views
33 follow
Forum:
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq
sequencing
papers
updated 6 months ago by
Ram
37k • written 7.0 years ago by
CandiceChuDVM
★ 2.4k
34
votes
15
replies
41k
views
8 follow
FPKM vs raw counts vs RPKM
counts
rpkm
raw
fpkm
RNA-Seq
updated 10 months ago by
Ram
37k • written 8.1 years ago by
NHEJ
▴ 330
3
votes
5
replies
41k
views
how to set the size of cell of heatmap.2 in R
heatmap.2
R
updated 11 months ago by
Ram
37k • written 8.2 years ago by
Zhilong Jia
★ 2.1k
38
votes
14
replies
41k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl
fasta
python
parsing
updated 9 months ago by
Michael Dondrup
52k • written 11.1 years ago by
Mohammad Reza Bakhtiarizadeh
▴ 350
1,000 results • Page
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Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
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68k
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Answer: how to do a reliable single cell sequencing analysis?
by
ATpoint
68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM
by
sanaz
• 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v
by
fuellen
▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM
by
Mike Smith
★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome
by
congliu37
• 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
by
Fabio Marroni
★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
by
Rob
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Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
by
Pierre Lindenbaum
152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence
by
vvasta
• 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
by
Fabio Marroni
★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
by
Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
by
Pierre Lindenbaum
152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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