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1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
23
votes
22
replies
36k
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 9 weeks ago by
Nicole
• 0 • written 4.7 years ago by
gaelgarcia
▴ 250
19
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 6 months ago by
Ram
37k • written 7.1 years ago by
dam4l
▴ 180
18
votes
19
replies
1.5k
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 9 weeks ago by
Ram
37k • written 4.1 years ago by
rbkh09
• 0
18
votes
7
replies
742
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
4 months ago by
Rafael Soler
★ 1.1k
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
14
votes
5
replies
2.6k
views
bioinformatics basic training
genome
Tutorial
updated 11 months ago by
Ram
37k • written 8.2 years ago by
f.muoghalu
• 0
12
votes
8
replies
542
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 4 months ago by
Matthias Zepper
2.9k • written 4 months ago by
A_heath
▴ 120
12
votes
13
replies
2.1k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 8 weeks ago by
Ram
37k • written 7.6 years ago by
sarathkurichiyil
• 0
11
votes
9
replies
2.0k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 6 weeks ago by
Ram
37k • written 7.6 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
10
votes
2
replies
332
views
any script that can do this task
shell-script
updated 10 months ago by
Ram
37k • written 10 months ago by
adyashapanda04
▴ 10
10
votes
5
replies
6.1k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 5 months ago by
Ram
37k • written 7.4 years ago by
seta
★ 1.7k
10
votes
11
replies
8.1k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 8 months ago by
Ram
37k • written 7.9 years ago by
SheelS
▴ 40
10
votes
8
replies
1.8k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 7 months ago by
Ram
37k • written 7.8 years ago by
friasoler
▴ 30
9
votes
2
replies
338
views
Answer needed urgently
Deep
updated 4 months ago by
Mensur Dlakic
★ 22k • written 4 months ago by
Deepak
• 0
9
votes
9
replies
1.2k
views
Which hg38 file?
reference
hg38
NCBI
updated 5 months ago by
appropiate
▴ 80 • written 6 months ago by
amy__
▴ 50
9
votes
1
reply
5.3k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq
macs
macs2
updated 5 months ago by
Ram
37k • written 7.3 years ago by
James Ashmore
★ 3.4k
9
votes
7
replies
719
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 29 days ago by
barslmn
★ 1.2k • written 4 weeks ago by
Batel
• 0
9
votes
7
replies
650
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA
ChIP
nf-core
ChIP-seq
updated 8 months ago by
Ram
37k • written 9 months ago by
2138493o
▴ 20
9
votes
4
replies
1.9k
views
[Code] Converte fasta/fa files to fastq
perl
fastq
sed
fasta
updated 5 months ago by
Ram
37k • written 7.2 years ago by
Shicheng Guo
★ 9.2k
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq
R
updated 4 weeks ago by
Ram
37k • written 7.7 years ago by
pbio
▴ 150
9
votes
14
replies
3.6k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 10 months ago by
Ram
37k • written 8.0 years ago by
hothriananya
▴ 70
9
votes
1
reply
3.2k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 5 months ago by
Ram
37k • written 7.7 years ago by
Niek De Klein
★ 2.6k
9
votes
4
replies
340
views
RNA seq, secreted protein
protein
gene
secreted
updated 7 weeks ago by
Joe
20k • written 8 weeks ago by
Rob
▴ 160
8
votes
11
replies
1.1k
views
using STAR instead of HISAT2
STAR
updated 6 months ago by
Ram
37k • written 6 months ago by
Chris
▴ 60
8
votes
3
replies
4.9k
views
Bioinformatics project for a beginner
projects
updated 6 months ago by
Ram
37k • written 7.1 years ago by
dharshank.1096
▴ 30
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 3 months ago by
Ram
37k • written 7.5 years ago by
biolab
★ 1.4k
8
votes
4
replies
1.7k
views
using different tools to identify differential exprssed genes
rna-seq
RNA-Seq
R
updated 4 months ago by
Ram
37k • written 7.4 years ago by
Anushka
▴ 20
8
votes
9
replies
2.0k
views
6 follow
Big difference in estimated duplicate reads between forward and reverse of paired-end RNA-seq
RNA-Seq
duplication
fastqc
updated 7 months ago by
rohitsatyam102
▴ 690 • written 3.2 years ago by
Eric Lim
★ 2.0k
8
votes
20
replies
1.7k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 8 months ago by
Ram
37k • written 4.5 years ago by
Bara'a
▴ 270
8
votes
3
replies
438
views
Package installation error using Bioconda
antismash
Bioconda
8 weeks ago by
A_heath
▴ 120
8
votes
9
replies
2.6k
views
error in rstudio
csv
matrix
rstudio
updated 4 months ago by
Ram
37k • written 7.5 years ago by
fi1d18
★ 4.1k
8
votes
5
replies
3.0k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM
FASTQ
updated 6 weeks ago by
Ram
37k • written 7.6 years ago by
Andrew
▴ 60
8
votes
6
replies
688
views
How to apply bioinformatic in vaccine design?
Vaccine
updated 11 weeks ago by
Dunois
★ 2.2k • written 11 weeks ago by
Jean
▴ 30
7
votes
7
replies
1.0k
views
LRT test with DESeq2 and how to interpret the results
significant
LRT
DESeq2
genes
RNA-Seq
updated 6 months ago by
krushnach80
★ 1.1k • written 8 months ago by
Maka
▴ 20
7
votes
8
replies
1.6k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock
gene-duplication
phylogeny
updated 11 hours ago by
Ram
37k • written 7.7 years ago by
xiaofeng.dong12
▴ 20
7
votes
10
replies
3.3k
views
Choosing phylogenetic approaches
phylogeny
updated 11 months ago by
Ram
37k • written 8.4 years ago by
Yongjie Zhang
▴ 100
7
votes
4
replies
3.2k
views
Abra for indel realignment
realignment
abra
gatk
updated 11 months ago by
Ram
37k • written 8.2 years ago by
Danielk
▴ 620
7
votes
8
replies
3.3k
views
remove duplicated entries from BLAST result file
blast
alignment
updated 6 weeks ago by
Ram
37k • written 7.7 years ago by
Kumar
▴ 150
7
votes
6
replies
2.1k
views
Optical duplicates?
duplicate
optical
updated 11 months ago by
flyamer
▴ 60 • written 20 months ago by
abascalfederico
★ 1.2k
7
votes
4
replies
1.3k
views
microarray gene datasets
gene
updated 14 hours ago by
Ram
37k • written 7.7 years ago by
bioinfo
▴ 60
7
votes
5
replies
3.6k
views
Trinity de novo transcript assembly too many transcripts
RNA-Seq
Assembly
updated 6 months ago by
Ram
37k • written 7.6 years ago by
Mehmet
▴ 780
7
votes
10
replies
3.7k
views
PSMC using haploid genomes
haploid
genome
PSMC
updated 11 months ago by
Ram
37k • written 8.2 years ago by
biogirl
▴ 200
7
votes
13
replies
3.6k
views
DESeq2: can I correct for relatedness when using data from multiplex families?
DESeq2
RNA-Seq
Multiplex-families
updated 9 months ago by
Ram
37k • written 8.0 years ago by
alesssia
▴ 580
7
votes
4
replies
927
views
Are there mm39/GRCm39 blacklist regions?
blacklist
8 months ago by
Ian
5.9k
7
votes
2
replies
3.1k
views
Counting reads for gene transcripts with overlapping loci
RNA-Seq
gene
R
updated 29 days ago by
Ram
37k • written 7.7 years ago by
Ruet
▴ 70
7
votes
4
replies
4.0k
views
IGV genome browser problems
igv
updated 8 weeks ago by
Ram
37k • written 7.6 years ago by
Marvin
▴ 210
7
votes
9
replies
700
views
Tools to check the length of isoforms in reference transcript
transcript
histogram
isoform
3 months ago by
Jjbox
▴ 30
7
votes
6
replies
1.1k
views
Perseus like missing value replacement in Python
Python
free
Data
LFQ-intensities
proteomics
analysis
Lable
11 months ago by
Balasubramaniam
▴ 20
7
votes
4
replies
2.0k
views
RSEM BAM outputs, which one to use for RSeQC?
RSEM
STAR
RSeQC
BAM
10 months ago by
Freek
▴ 50
7
votes
7
replies
918
views
GSEA analysis
Hi
updated 9 months ago by
cvenkat95
▴ 10 • written 9 months ago by
sarahawan92
▴ 10
1,000 results • Page
1 of 20
Recent Votes
Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
The Biostar Handbook. A bioinformatics e-book for beginners.
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Answer: What is the difference between a Read and a Fragment in RNA-seq?
lncRNA analysis tutorial
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
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Comment: How to extract the list of genes from TCGA CNV data
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Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
Comment: RNASeq differential expression masked by pathways disregulation
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If this is the case then you cannot correct for anything as this effect is nested with center.
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★ 1.2k
That error message is very descriptive. Could you also add the line 997531?
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Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…
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Hello #gubrins Have you found the answer
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Using [**Entrezdirect**][1]. Date in last column is collection date. No way to query using it though. Could be wrong. $ esearch -db nu…
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Pretty sure that nothing other than HHsuite outputs results in `.hhr` format.
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Same allele = weight of 1, different allele = weight of 0. You can read more here: https://choishingwan.github.io/PRS-Tutorial/plink/#gener…
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Hi jv, Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I…
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by
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What is 'peaks' entered as?... The input is: CoveragePlot( object = pbmc, region = "CD8A", ranges = peaks, …
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I totally get your point, maybe long-winded was also not the right description for my issue. One example, [custom databases][1] are very cl…
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Wouldn't you take your MACS2 files, import them with rtracklayer so that they are GRanges objects, and then pass those as the peaks? i.e. w…
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Honestly, I think most RNASeq aligners are fairly robust to adapters. You could probably get away with not trimming at all
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