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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
39
votes
38
replies
6.8k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 5 months ago by
Ram
37k • written 7.2 years ago by
John
13k
220
votes
38
replies
132k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 6 weeks ago by
harelarik
▴ 90 • written 9.9 years ago by
Malachi Griffith
19k
164
votes
38
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
written 11.6 years ago by
Palu
▴ 240
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 9 months ago by
Ram
37k • written 8.0 years ago by
Mo
▴ 920
89
votes
38
replies
123k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 4 months ago by
Wang Cong
▴ 10 • written 10.6 years ago by
abi
▴ 370
159
votes
38
replies
14k
views
22 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
bioinformatics
Forum
humor
updated 4 months ago by
Ambu Vijayan
▴ 30 • written 9.8 years ago by
Istvan Albert
96k
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
49
votes
36
replies
7.1k
views
11 follow
Forum:
New features and bug fixes for Biostar to work on during Google Summer of Code
gsoc
meta
biostar
feature
bug
updated 4 months ago by
Ram
37k • written 8.7 years ago by
Paolo
▴ 110
8
votes
36
replies
9.6k
views
18 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 8 weeks ago by
Ram
37k • written 7.6 years ago by
kevluv93
▴ 160
99
votes
36
replies
26k
views
32 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 5 days ago by
Jeremy Leipzig
21k • written 9.2 years ago by
14134125465346445
★ 3.6k
9
votes
36
replies
2.4k
views
6 follow
GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip)
R
updated 11 weeks ago by
seta
★ 1.7k • written 2.2 years ago by
daniela.paola.s.p
▴ 30
59
votes
36
replies
33k
views
27 follow
Pca From Vcf Files
pca
genome
vcf
updated 5 months ago by
hewm2008
▴ 40 • written 10.7 years ago by
Rubal7
▴ 820
251
votes
36
replies
30k
views
27 follow
Forum:
How Do You Manage Your Files & Directories For Your Projects ?
file
updated 4 months ago by
Kevin Blighe
84k • written 12.8 years ago by
Pierre Lindenbaum
152k
84
votes
36
replies
16k
views
13 follow
Forum:
Benchmark - Comparison of Different NGS Mappers
mRNA-Seq
benchmark
NGS-mapper
updated 10 months ago by
Ram
37k • written 8.1 years ago by
David Langenberger
9.8k
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
22
votes
35
replies
4.5k
views
Removing identifier with "unavailable sequence" from FASTA file
sequence
genome
blast
RNA-Seq
updated 10 months ago by
Ram
37k • written 8.0 years ago by
seta
★ 1.7k
65
votes
35
replies
18k
views
17 follow
Which Dna Compression Algorithms Are Actually Used?
dna
updated 5 months ago by
Pierre Lindenbaum
152k • written 11.7 years ago by
Anthony Labarre
▴ 270
45
votes
35
replies
4.5k
views
12 follow
Forum:
looking for a bioinformatics project to do during military rotation
military
updated 7 months ago by
Ram
37k • written 5.4 years ago by
hasani.iut6
▴ 60
83
votes
34
replies
15k
views
21 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
R
pathway
enrichment
active subnetwork
Tutorial
updated 6 months ago by
Ram
37k • written 4.6 years ago by
egeulgen
★ 1.3k
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
80
votes
34
replies
3.9k
views
11 follow
Forum:
Authorship issues- how to resolve?
authorship
updated 24 days ago by
Ram
37k • written 7.7 years ago by
datanerd
▴ 500
15
votes
34
replies
10k
views
Improving efficiency of awk for large files
awk
updated 3 months ago by
Ram
37k • written 7.5 years ago by
AW
▴ 350
41
votes
34
replies
9.1k
views
7 follow
Technical replicates in RNAseq
RNA-Seq
technical_replicates
11 months ago by
grant.hovhannisyan
★ 2.5k
25
votes
34
replies
28k
views
15 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 6 months ago by
Ram
37k • written 8.9 years ago by
komal.rathi
★ 4.0k
62
votes
34
replies
23k
views
20 follow
Phylogenetic Analysis Of Whole Genomes
phylogenetics
tree
updated 10 months ago by
Ram
37k • written 12.5 years ago by
Aparna
▴ 120
16
votes
34
replies
11k
views
6 follow
Why am I unable to load my data from a tab separated file into R?
microarray
programming
R
updated 9 months ago by
Ram
37k • written 8.0 years ago by
Mo
▴ 920
19
votes
34
replies
4.2k
views
6 follow
How can I convert the blast results into a matrix?
perl
linux
python
blast
updated 11 months ago by
Ram
37k • written 8.2 years ago by
kandoigaurav
▴ 150
68
votes
33
replies
15k
views
18 follow
Choosing Random Set Of Seqs From Larger Set
random
fasta
updated 9 months ago by
Ram
37k • written 10.9 years ago by
razor
▴ 190
11
votes
33
replies
16k
views
How we can analyze sanger sequence chromatogram?
SNP
sequencing
alignment
sanger
updated 11 months ago by
Ram
37k • written 8.2 years ago by
Elnaaz
▴ 40
274
votes
33
replies
90k
views
24 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
tutorial
Tutorial
updated 12 months ago by
tshtatland
▴ 100 • written 9.3 years ago by
Obi Griffith
20k
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
12
votes
33
replies
6.5k
views
9 follow
Back-filling missing genotypes in merged VCF
vcf
updated 5 weeks ago by
Pierre Lindenbaum
152k • written 8.2 years ago by
Katie D'Aco
★ 1.0k
88
votes
32
replies
8.0k
views
11 follow
Forum:
Vintage / unconventional pictures for Bioinformatics
history
picture
updated 10 months ago by
Ram
37k • written 8.3 years ago by
Pierre Lindenbaum
152k
129
votes
32
replies
120k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 9 months ago by
Ram
37k • written 11.9 years ago by
Gon
▴ 530
53
votes
32
replies
11k
views
13 follow
Bio-Javascript?
updated 9 months ago by
Ram
37k • written 11.9 years ago by
Lee Katz
★ 3.1k
70
votes
31
replies
24k
views
10 follow
Illumina Instrument Type from fastq?
fastq
updated 5 months ago by
GenoMax
125k • written 6.6 years ago by
andrew.j.skelton73
6.5k
93
votes
31
replies
94k
views
20 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 11 months ago by
Dan
▴ 60 • written 10.7 years ago by
GPR
▴ 380
89
votes
31
replies
11k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs
visualization
genomics
updated 6 months ago by
Ram
37k • written 10.9 years ago by
John
★ 1.5k
97
votes
31
replies
79k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 6 months ago by
Ram
37k • written 11.6 years ago by
2184687-1231-83-
★ 5.0k
12
votes
31
replies
4.5k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
gene
geneset
abinitio
Tutorial
genome
3 months ago by
Juke34
7.5k
7
votes
31
replies
13k
views
Scale and Center [normalized] RNA-seq expression counts for PCA ?
sequencing
pca
genome
R
RNA-Seq
updated 9 months ago by
Ram
37k • written 7.9 years ago by
gaelgarcia
▴ 250
3
votes
31
replies
2.2k
views
Extract reads from BAM file with known variant
bam
variant
samtools
6 months ago by
pablo
▴ 230
116
votes
31
replies
35k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 7 months ago by
Ram
37k • written 9.4 years ago by
Eric Normandeau
11k
45
votes
31
replies
8.0k
views
6 follow
What Improvements Would You Recommend For This Genome Scaffolding Software?
genome
scaffolding
next-gen-sequencing
updated 6 months ago by
Ram
37k • written 11.9 years ago by
Michael Barton
★ 1.8k
94
votes
31
replies
36k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python
alignment
next-gen
sequencing
database
updated 10 months ago by
Ram
37k • written 12.4 years ago by
User 1586
▴ 280
2
votes
30
replies
9.3k
views
6 follow
Genomic Restriction Finder
fasta
updated 11 months ago by
Ram
37k • written 9.2 years ago by
rhasbunz
▴ 20
60
votes
30
replies
30k
views
13 follow
Remove mitochondrial reads from BAM files
awk
samtools
BAM
RNA-Seq
updated 9 months ago by
Ram
37k • written 8.0 years ago by
enricoferrero
▴ 880
140
votes
30
replies
123k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 4 months ago by
Ram
37k • written 10.9 years ago by
Anima Mundi
★ 2.9k
41
votes
30
replies
21k
views
24 follow
Is There A List Of Top N Bioinformatics Or Genome Software Company Or Studio ?
genome
software
updated 6 months ago by
Ram
37k • written 11.6 years ago by
Gentle Yang
▴ 190
17
votes
30
replies
28k
views
8 follow
Getting A Vcf File From A Fasta Alignment
vcf
fasta
conversion
alignment
updated 9 months ago by
Ram
37k • written 8.9 years ago by
Bioch'Ti
★ 1.1k
1,000 results • Page
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Recent Votes
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Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
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ATpoint
68k
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tianshenbio
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maxdlf12
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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
▴ 160
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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