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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
18
votes
27
replies
18k
views
20 follow
Where Can I Download Vcf Files For Publicly Available Data?
vcf
snp
updated 8 months ago by
Ram
41k • written 12.0 years ago by
Kevin
▴ 640
197
votes
27
replies
33k
views
20 follow
Forum:
Bioinformatics Cartoon
bioinformatics
updated 4 months ago by
Ram
41k • written 11.9 years ago by
Maxime Lamontagne
★ 2.3k
98
votes
27
replies
84k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 6 months ago by
NIRJHAR
• 0 • written 11.5 years ago by
Rubal7
▴ 830
49
votes
27
replies
6.7k
views
10 follow
Forum:
Possible augmented reality tools for bioinformatics and current problems
visualization
3D
augmented-reality
updated 8 months ago by
Ram
41k • written 8.1 years ago by
Peter Leontev
▴ 90
65
votes
27
replies
6.9k
views
14 follow
Forum:
What is the reason for most software errors in Bioinformatics according to you?
software-error
blast
sequencing
SNP
R
updated 8 months ago by
Ram
41k • written 7.7 years ago by
harne.priyanka
▴ 110
28
votes
27
replies
14k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython
python
fastq
next-gen-sequencing
updated 21 days ago by
Ram
41k • written 13.6 years ago by
Darked89
4.5k
53
votes
27
replies
4.0k
views
11 follow
Should General Programming Questions Actually Be Posted To Biostar?
meta
biostars
updated 9 months ago by
Ram
41k • written 12.4 years ago by
Pablo Pareja
★ 1.6k
30
votes
27
replies
2.4k
views
11 follow
Forum:
How do you spend your time (productively) when your script is running?
time-management
updated 7 months ago by
Ram
41k • written 6.8 years ago by
venu
7.1k
41
votes
27
replies
5.5k
views
8 follow
Forum:
Why bioinformaticians need to know programming languages?
Python
R
Programming
updated 6 months ago by
Ram
41k • written 6.5 years ago by
nilo
▴ 90
27
votes
27
replies
10.0k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp
allele
biomart
dbsnp
updated 24 days ago by
Ram
41k • written 13.7 years ago by
Michael
53k
3
votes
27
replies
2.2k
views
7 follow
Forum:
What server do you use?
HPC
AWS
updated 6 months ago by
Ram
41k • written 5.4 years ago by
caggtaagtat
★ 1.8k
63
votes
27
replies
26k
views
18 follow
Data Too Big To Be Stored In Memory: Common Options
python
updated 9 months ago by
Ram
41k • written 11.0 years ago by
Click downvote
▴ 720
76
votes
26
replies
112k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 8 days ago by
cschu181
★ 2.8k • written 8.6 years ago by
Chenglin
▴ 260
171
votes
26
replies
7.5k
views
12 follow
How Do You Acknowledge Biostar And Its Contributors In Your Research Output?
meta
biostars
updated 9 months ago by
Ram
41k • written 12.8 years ago by
Andra Waagmeester
3.2k
24
votes
26
replies
2.0k
views
6 follow
Forum:
Organizing a Bioinformatics Conference ?
meeting
conference
updated 6 months ago by
Ram
41k • written 6.0 years ago by
Pierre Lindenbaum
158k
6
votes
26
replies
9.1k
views
Realign BAM files to other reference file
bam
samtools
updated 8 months ago by
Ram
41k • written 5.4 years ago by
marongiu.luigi
▴ 690
9
votes
26
replies
9.1k
views
GREP: out of memory
Deseq2
macOS
gff
HEloci
updated 8 months ago by
Ram
41k • written 5.4 years ago by
jaqx008
▴ 110
25
votes
26
replies
3.6k
views
warning in R
R
updated 11 months ago by
Ram
41k • written 8.5 years ago by
fi1d18
★ 4.2k
136
votes
26
replies
24k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix
perl
genomics
updated 9 months ago by
Ram
41k • written 11.9 years ago by
Brett Thomas
▴ 300
8
votes
26
replies
4.2k
views
Fasta sequence replacement based on header name
alignment
Assembly
sequencing
RNA-Seq
updated 11 months ago by
Ram
41k • written 8.4 years ago by
seta
★ 1.8k
47
votes
26
replies
3.7k
views
11 follow
Blog:
Evolution of Biostars
meta
Biostars
updated 3 months ago by
aldhairmedico
▴ 70 • written 4.8 years ago by
venu
7.1k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner
snp
sequencing
updated 21 days ago by
Ram
41k • written 13.7 years ago by
Pierre Lindenbaum
158k
64
votes
26
replies
13k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 8 months ago by
Ram
41k • written 6.2 years ago by
Kevin Blighe
86k
17
votes
26
replies
2.0k
views
File conversion in bash, discrepancy in number of lines after conversion.
bash
updated 8 months ago by
Ram
41k • written 3.6 years ago by
ATCG
▴ 380
105
votes
26
replies
41k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 10 weeks ago by
zx8754
11k • written 10.9 years ago by
henryvuong
▴ 810
3
votes
26
replies
1.4k
views
6 follow
STAR Genome index Error
STAR
updated 8 weeks ago by
Ram
41k • written 8 weeks ago by
Prasanna
• 0
81
votes
26
replies
12k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 5 weeks ago by
Ram
41k • written 13.7 years ago by
User 59
13k
65
votes
26
replies
13k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 8 months ago by
Ram
41k • written 4.7 years ago by
finswimmer
16k
20
votes
26
replies
2.8k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment
fasta
image
updated 4 months ago by
Joe
21k • written 4.5 years ago by
Joel Wallenius
▴ 180
72
votes
26
replies
27k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 9 months ago by
Ram
41k • written 9.8 years ago by
Istvan Albert
99k
5
votes
26
replies
6.7k
views
Pre-computed list of genes in LD with a SNP with r2 from 1000Genomes / hg19
genomics
snp
ld
updated 11 months ago by
Ram
41k • written 9.3 years ago by
Khader Shameer
18k
24
votes
26
replies
3.2k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 5 months ago by
Ram
41k • written 4.1 years ago by
German.M.Demidov
★ 2.9k
37
votes
26
replies
4.3k
views
7 follow
Ngs Challenge: Can You Give An Insight About This Imaginary Genetic Disease ?
next-gen-sequencing
updated 9 months ago by
Ram
41k • written 12.0 years ago by
Pierre Lindenbaum
158k
33
votes
26
replies
3.4k
views
7 follow
Forum:
Poll: How many people have PyPy?
pypy
python
updated 8 months ago by
Ram
41k • written 7.7 years ago by
John
13k
18
votes
26
replies
16k
views
16 follow
bedtools coverage gives error received illegal bin number, but that number isn't in my data!
ChIP-Seq
bedtools
updated 10 months ago by
Ram
41k • written 6.8 years ago by
tara.alpert
▴ 40
118
votes
26
replies
34k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 8 months ago by
e.r.zakiev
▴ 170 • written 8.5 years ago by
mhockin
▴ 610
4
votes
26
replies
17k
views
10 follow
ADMIXTURE and R, color meaning on barplot in studing population ancestry, K value
R
gene
updated 9 months ago by
dr.fakharunnisa
• 0 • written 8.2 years ago by
dirranrak
▴ 20
65
votes
26
replies
19k
views
13 follow
Forum:
Macosx For Bioinformatics?
linux
updated 9 months ago by
Ram
41k • written 10.0 years ago by
Eric Normandeau
11k
7
votes
25
replies
10k
views
6 follow
Tool:
MIGEC: towards error-free profiling of immune repertoires
sequencing-error
tcr
antibody
molecular-barcode
updated 5 months ago by
Ram
41k • written 9.6 years ago by
mikhail.shugay
3.5k
95
votes
25
replies
32k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Istvan Albert
99k
69
votes
25
replies
6.7k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 24 days ago by
Ram
41k • written 13.7 years ago by
Dave Gerrard
▴ 190
38
votes
25
replies
8.5k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 11 weeks ago by
Ram
41k • written 7.7 years ago by
waqasnayab
▴ 250
13
votes
25
replies
3.8k
views
7 follow
VEP output has no gene names
alignment
sequencing
vep
updated 6 months ago by
barslmn
★ 2.0k • written 5.3 years ago by
Gene_MMP8
▴ 230
13
votes
25
replies
11k
views
9 follow
Tool:
Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis
sequencing
ngs
updated 5 months ago by
Ram
41k • written 10.3 years ago by
mikhail.shugay
3.5k
59
votes
25
replies
4.2k
views
8 follow
Forum:
Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size
statistical-power
RNA-Seq
updated 5 months ago by
Ram
41k • written 3.3 years ago by
telroyjatter
▴ 220
17
votes
25
replies
2.1k
views
Tool:
Platform for Bioinformatics Students, Scholars and Scientists
sequence
genome
updated 5 months ago by
Ram
41k • written 7.8 years ago by
support
▴ 50
16
votes
25
replies
12k
views
13 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 5 months ago by
Pierre Lindenbaum
158k • written 22 months ago by
ConvolutedGenome
▴ 20
58
votes
25
replies
39k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 8 months ago by
Ram
41k • written 7.3 years ago by
Shicheng Guo
★ 9.3k
39
votes
25
replies
4.0k
views
9 follow
Forum:
Making a mac book Bioinfo ready (El Capitan)
mac
software-installation
updated 8 months ago by
Ram
41k • written 7.7 years ago by
Eric Normandeau
11k
23
votes
25
replies
2.6k
views
bash and awk code
bash
awk
terminal
11 months ago by
Sam
▴ 150
1,000 results • Page
4 of 20
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
by
swbarnes2
13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
fluke
• 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts
by
Istvan Albert
99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
beausoleilmo
▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
CTLong
▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC
by
ayasu
• 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts
by
Brian Bushnell
19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
Brian Bushnell
19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters?
by
AMARU
• 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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