Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
23
votes
22
replies
38k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 3 months ago by
Nicole
• 0 • written 4.9 years ago by
gaelgarcia
▴ 250
20
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 8 months ago by
Ram
38k • written 7.2 years ago by
dam4l
▴ 190
18
votes
19
replies
1.6k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 3 months ago by
Ram
38k • written 4.2 years ago by
rbkh09
• 0
18
votes
7
replies
810
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
6 months ago by
Rafael Soler
★ 1.1k
18
votes
4
replies
8.1k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 4 weeks ago by
Ram
38k • written 9.7 years ago by
user
▴ 930
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 11 months ago by
Ram
38k • written 8.1 years ago by
Mo
▴ 920
14
votes
5
replies
2.7k
views
bioinformatics basic training
genome
updated 16 days ago by
Ram
38k • written 8.3 years ago by
f.muoghalu
• 0
12
votes
8
replies
605
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 6 months ago by
Matthias Zepper
3.4k • written 6 months ago by
A_heath
▴ 120
12
votes
13
replies
2.1k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 3 months ago by
Ram
38k • written 7.7 years ago by
sarathkurichiyil
• 0
11
votes
9
replies
2.1k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 3 months ago by
Ram
38k • written 7.8 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 8 days ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
10
votes
11
replies
8.2k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 10 months ago by
Ram
38k • written 8.0 years ago by
SheelS
▴ 40
10
votes
8
replies
1.9k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 9 months ago by
Ram
38k • written 8.0 years ago by
friasoler
▴ 30
10
votes
5
replies
6.3k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 7 months ago by
Ram
38k • written 7.6 years ago by
seta
★ 1.8k
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 7 days ago by
Ram
38k • written 4.5 years ago by
marongiu.luigi
▴ 670
9
votes
7
replies
783
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 12 weeks ago by
barslmn
★ 1.4k • written 12 weeks ago by
Batel
• 0
9
votes
2
replies
363
views
Answer needed urgently
Deep
updated 6 months ago by
Mensur Dlakic
★ 23k • written 6 months ago by
Deepak
• 0
9
votes
1
reply
3.2k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 7 months ago by
Ram
38k • written 7.8 years ago by
Niek De Klein
★ 2.6k
9
votes
1
reply
5.4k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq
macs
macs2
updated 7 months ago by
Ram
38k • written 7.4 years ago by
James Ashmore
★ 3.4k
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq
R
updated 12 weeks ago by
Ram
38k • written 7.8 years ago by
pbio
▴ 150
9
votes
9
replies
1.4k
views
Which hg38 file?
reference
hg38
NCBI
updated 7 months ago by
appropiate
▴ 80 • written 8 months ago by
amy__
▴ 50
9
votes
4
replies
406
views
RNA seq, secreted protein
protein
gene
secreted
updated 3 months ago by
Joe
20k • written 3 months ago by
Rob
▴ 160
9
votes
14
replies
3.7k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 12 months ago by
Ram
38k • written 8.2 years ago by
hothriananya
▴ 70
9
votes
7
replies
689
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA
ChIP
nf-core
ChIP-seq
updated 10 months ago by
Ram
38k • written 11 months ago by
2138493o
▴ 20
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 7 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 7 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
4
replies
1.9k
views
[Code] Converte fasta/fa files to fastq
perl
fastq
sed
fasta
updated 7 months ago by
Ram
38k • written 7.4 years ago by
Shicheng Guo
★ 9.3k
8
votes
3
replies
534
views
Package installation error using Bioconda
antismash
Bioconda
3 months ago by
A_heath
▴ 120
8
votes
2
replies
5.5k
views
Differential gene expression analysis in Python
python
R
updated 7 weeks ago by
Ram
38k • written 17 months ago by
Leendert
▴ 30
8
votes
3
replies
5.0k
views
Bioinformatics project for a beginner
projects
updated 8 months ago by
Ram
38k • written 7.3 years ago by
dharshank.1096
▴ 30
8
votes
4
replies
1.7k
views
using different tools to identify differential exprssed genes
rna-seq
RNA-Seq
R
updated 6 months ago by
Ram
38k • written 7.6 years ago by
Anushka
▴ 20
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 8 days ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
8
votes
13
replies
765
views
Mapped reads not mapping to a real sequence?
bam
sam
samtools
kallisto
6 weeks ago by
txema.heredia
▴ 70
8
votes
9
replies
2.6k
views
error in rstudio
csv
matrix
rstudio
updated 6 months ago by
Ram
38k • written 7.6 years ago by
fi1d18
★ 4.1k
8
votes
5
replies
3.1k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM
FASTQ
updated 3 months ago by
Ram
38k • written 7.8 years ago by
Andrew
▴ 60
8
votes
11
replies
1.2k
views
using STAR instead of HISAT2
STAR
updated 8 months ago by
Ram
38k • written 8 months ago by
Chris
▴ 70
8
votes
9
replies
2.1k
views
6 follow
Big difference in estimated duplicate reads between forward and reverse of paired-end RNA-seq
RNA-Seq
duplication
fastqc
updated 9 months ago by
rohitsatyam102
▴ 690 • written 3.4 years ago by
Eric Lim
★ 2.0k
8
votes
12
replies
2.5k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 12 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
8
votes
20
replies
1.8k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 10 months ago by
Ram
38k • written 4.7 years ago by
Bara'a
▴ 270
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 4 months ago by
Ram
38k • written 7.7 years ago by
biolab
★ 1.4k
8
votes
6
replies
759
views
How to apply bioinformatic in vaccine design?
Vaccine
updated 4 months ago by
Dunois
★ 2.3k • written 4 months ago by
Jean
▴ 50
7
votes
4
replies
1.2k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment
RNA-Seq
R
updated 15 days ago by
Ram
38k • written 4.7 years ago by
healing80
• 0
7
votes
9
replies
772
views
Tools to check the length of isoforms in reference transcript
transcript
histogram
isoform
5 months ago by
Jjbox
▴ 40
7
votes
8
replies
1.7k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock
gene-duplication
phylogeny
updated 7 weeks ago by
Ram
38k • written 7.9 years ago by
xiaofeng.dong12
▴ 20
7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 7 days ago by
Ram
38k • written 16 months ago by
Nikhil
▴ 10
7
votes
8
replies
3.4k
views
remove duplicated entries from BLAST result file
blast
alignment
updated 3 months ago by
Ram
38k • written 7.8 years ago by
Kumar
▴ 150
7
votes
4
replies
4.0k
views
IGV genome browser problems
igv
updated 3 months ago by
Ram
38k • written 7.7 years ago by
Marvin
▴ 210
7
votes
7
replies
961
views
GSEA analysis
Hi
updated 11 months ago by
cvenkat95
▴ 10 • written 11 months ago by
sarahawan92
▴ 10
7
votes
4
replies
1.1k
views
Error: missing values and NaN's not allowed if 'na.rm' is FALSE
Genome
Software
8 months ago by
sunnykevin97
▴ 970
7
votes
4
replies
1.7k
views
useful and freely available softwares for Bioinformatics
software
updated 12 days ago by
Ram
38k • written 8.0 years ago by
Mo
▴ 920
1,000 results • Page
1 of 20
Recent Votes
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
Answer: Somatic truth set
Recent Locations •
All
United States,
just now
Pakistan,
1 minute ago
South Korea,
5 minutes ago
Palo Alto, CA, USA,
11 minutes ago
South Korea,
12 minutes ago
United States,
21 minutes ago
State College, PA, Penn State,
27 minutes ago
Recent Awards •
All
Popular Question
to
Bogdan
★ 1.3k
Popular Question
to
pavelasquezv
▴ 50
Popular Question
to
Anand Rao
▴ 550
Scholar
to
andres.firrincieli
3.2k
Scholar
to
Jesse
• 0
Popular Question
to
chaco001
▴ 10
Scholar
to
Jaykumar
▴ 50
Recent Replies
Answer: Align miRNA library (small RNA-seq) without trimming
by
Ming Tommy Tang
★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression
by
afei
• 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa
by
rebeliscu
▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
by
cfos4698
▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking
by
Mensur Dlakic
★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error
by
Declan
• 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq
by
dsull
★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set
by
lethalfang
▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
Comment: GO enrichment analysis
by
Jeremy
▴ 780
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job?
by
Carambakaracho
★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
Traffic: 1629 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6