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1,000 results • Page
6 of 20
Sort: replies
Rank
Views
Votes
Replies
38
votes
31
replies
2.8k
views
10 follow
Forum:
To the Biologists out there: What bioinf tool are you missing?
education
career
updated 12 months ago by
Ram
43k • written 7.8 years ago by
mschmid
▴ 180
17
votes
31
replies
5.7k
views
Finding the best model for expression data (RNA-Seq counts)
RNA-Seq
glm
model fit
regression
updated 5.1 years ago by
i.sudbery
19k • written 5.1 years ago by
User 7754
▴ 250
31
votes
31
replies
2.1k
views
collecting ultraconserved elements from RNA-seq data
RNA-Seq
sequence
genome
updated 7.7 years ago by
BioinfGuru
★ 1.7k • written 7.7 years ago by
Farbod
★ 3.4k
14
votes
31
replies
5.0k
views
9 follow
make fasta sequence which is multiple of three
alignment
6.0 years ago by
alim.hcu
▴ 20
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
18
votes
31
replies
8.5k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff
parse
updated 13 months ago by
Juke34
8.5k • written 5.6 years ago by
a.rex
▴ 350
105
votes
31
replies
94k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 4 months ago by
mmfansler
▴ 450 • written 12.8 years ago by
2184687-1231-83-
★ 5.1k
120
votes
31
replies
199k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
11
votes
31
replies
14k
views
6 follow
How to concatenate multiple fasta file
sequence
genome
updated 11 months ago by
doggie
• 0 • written 5.7 years ago by
fec2
▴ 50
11
votes
31
replies
7.9k
views
Using wildcards to accept paired-end reads from Snakemake
snakemake
WGS
3.9 years ago by
moldach686
▴ 90
78
votes
31
replies
6.8k
views
14 follow
Forum:
Do Bad Questions Even Exist?
biostars
general
education
updated 14 months ago by
Ram
43k • written 13.2 years ago by
Chris Evelo
10k
89
votes
31
replies
14k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs
visualization
genomics
updated 21 months ago by
Ram
43k • written 12.1 years ago by
John
★ 1.5k
53
votes
31
replies
6.6k
views
15 follow
Biostar Flyer For Outreach
biostars
updated 14 months ago by
Ram
43k • written 13.5 years ago by
Mary
11k
30
votes
31
replies
3.8k
views
11 follow
Forum:
I need your help to find my future
internship
masters
career
updated 12 months ago by
Ram
43k • written 7.8 years ago by
Baptiste
▴ 90
10
votes
31
replies
4.5k
views
7 follow
Extract columns from a vcf file using identifiers from a second file
snp
updated 2.5 years ago by
GenoMax
141k • written 6.0 years ago by
paraskevopou
▴ 20
3
votes
31
replies
4.1k
views
Extract reads from BAM file with known variant
bam
variant
samtools
21 months ago by
pablo
▴ 300
14
votes
31
replies
13k
views
6 follow
De-duplicate UMI at FASTQ level
UMI
fastq
updated 5.3 years ago by
Rituriya
▴ 40 • written 5.5 years ago by
jomo018
▴ 720
6
votes
31
replies
9.8k
views
16 follow
Cnv Calling Methods For The Illumina Omni2.5 - Penncnv And Quantisnp Possible?
cnv
illumina
copynumber
updated 10.7 years ago by
swrdyani
• 0 • written 12.6 years ago by
Ryan D
★ 3.4k
46
votes
31
replies
18k
views
15 follow
Bwa Mem Have Different Alignment Result When Using Different Threads
updated 5.1 years ago by
grant.hovhannisyan
★ 2.6k • written 10.3 years ago by
shl198
▴ 440
147
votes
31
replies
137k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 9 months ago by
Ram
43k • written 12.2 years ago by
Anima Mundi
★ 2.9k
13
votes
31
replies
3.8k
views
Feature extraction from DNA sequence
snp
machine learning
deep learning
updated 5.1 years ago by
pltbiotech_tkarthi
▴ 180 • written 5.4 years ago by
bioinfo456
▴ 150
94
votes
31
replies
39k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python
alignment
next-gen
sequencing
database
updated 2.1 years ago by
Ram
43k • written 13.7 years ago by
User 1586
▴ 280
7
votes
31
replies
15k
views
Scale and Center [normalized] RNA-seq expression counts for PCA ?
sequencing
pca
genome
R
RNA-Seq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
gaelgarcia
▴ 260
14
votes
31
replies
6.8k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 13 months ago by
Ram
43k • written 4.7 years ago by
Juke34
8.5k
17
votes
30
replies
3.5k
views
7 follow
Update third line in fastq file using Biopython
fastq
updated 7.3 years ago by
Alex Reynolds
35k • written 7.3 years ago by
spaladug
▴ 10
3
votes
30
replies
11k
views
6 follow
Genomic Restriction Finder
fasta
updated 2.2 years ago by
Ram
43k • written 10.5 years ago by
rhasbunz
▴ 30
19
votes
30
replies
7.4k
views
6 follow
How To Retrieve Gene Variations From Ensembl Using The Perl Api?
ensembl
variation
perl
api
updated 6.0 years ago by
Biostar
20 • written 13.2 years ago by
Jarretinha
3.4k
13
votes
30
replies
5.5k
views
Is it appropriate to assume genes of similar expression level also have similar variance?
deseq
differential-expression
updated 6.3 years ago by
Santosh Anand
5.7k • written 6.3 years ago by
-_-
★ 1.1k
13
votes
30
replies
8.5k
views
10 follow
BagFoot TF foot printing
R
bagfoot
bagfootr
ChIP-Seq
updated 5.6 years ago by
Ashley Stephen Doane
▴ 20 • written 6.5 years ago by
rbronste
▴ 420
15
votes
30
replies
12k
views
6 follow
annotation of SV (structural variants)
SV
annotation
updated 4.3 years ago by
Fire
• 0 • written 6.3 years ago by
Bogdan
★ 1.4k
47
votes
30
replies
4.3k
views
10 follow
Forum:
Bioinformatics software distribution
software
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
41
votes
30
replies
23k
views
24 follow
Is There A List Of Top N Bioinformatics Or Genome Software Company Or Studio ?
genome
software
updated 21 months ago by
Ram
43k • written 12.9 years ago by
Gentle Yang
▴ 190
9
votes
30
replies
11k
views
small RNA-seq pipelines
small-RNA-seq
pipelines
updated 24 months ago by
Ram
43k • written 9.2 years ago by
Saad Khan
▴ 440
48
votes
30
replies
14k
views
11 follow
Determine Whether A Gene Product Is A Transcription Factor
transcription
gene
updated 13.3 years ago by
Obi Griffith
20k • written 13.7 years ago by
Mike Dewar
★ 1.6k
4
votes
30
replies
2.4k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 3.7 years ago by
Ram
43k • written 3.7 years ago by
sami
▴ 40
65
votes
30
replies
35k
views
13 follow
Remove mitochondrial reads from BAM files
awk
samtools
BAM
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.2 years ago by
enricoferrero
▴ 900
4
votes
30
replies
2.3k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
3.8 years ago by
stan.aanhane
▴ 30
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Khader Shameer
18k
43
votes
30
replies
15k
views
11 follow
Extract Fasta Sequences Sub Sets
fasta
updated 8.1 years ago by
Stephane Plaisance
▴ 460 • written 10.6 years ago by
prp291
▴ 70
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 10 months ago by
Ram
43k • written 5.9 years ago by
Jennifer Pham
▴ 450
33
votes
30
replies
33k
views
9 follow
Converting Bam To Bedgraph For Viewing On Ucsc?
bedtools
bam
bed
ucsc
genome-browser
updated 2.5 years ago by
Maximilian Haeussler
★ 1.6k • written 11.2 years ago by
user
▴ 940
15
votes
30
replies
3.5k
views
how to retrieve specific raws from a data matrix based on Affymetrix ID in Linux
affymetrix
linux
matrix
updated 2.1 years ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
25
votes
30
replies
7.5k
views
8 follow
Searching For Mouse Regulatory Motifs
gene
motif
motif
transcription
updated 13.9 years ago by
Ejm
• 0 • written 13.9 years ago by
Andrew Su
4.9k
16
votes
30
replies
54k
views
9 follow
Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
dna
sequence
retrieval
perl
bioperl
updated 13.2 years ago by
Palu
▴ 290 • written 13.2 years ago by
Samad
▴ 90
18
votes
30
replies
33k
views
8 follow
Getting A Vcf File From A Fasta Alignment
vcf
fasta
conversion
alignment
updated 2.0 years ago by
Ram
43k • written 10.2 years ago by
Bioch'Ti
★ 1.1k
8
votes
30
replies
5.1k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.1 years ago by
wm
▴ 560 • written 4.1 years ago by
Researcher
▴ 20
62
votes
30
replies
8.4k
views
14 follow
Online Resources For Mouse Research
mouse
online
database
genetics
genomics
updated 7.5 years ago by
LLTommy
★ 1.2k • written 12.3 years ago by
Andrew Su
4.9k
34
votes
30
replies
2.9k
views
6 follow
Tool:
BioFlows - Container-enabled Bioinformatics pipeline engine
workflow
next-gen
RNA-Seq
pipeline
updated 13 months ago by
Ram
43k • written 3.4 years ago by
drsami
▴ 90
174
votes
30
replies
92k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 2.3 years ago by
Ram
43k • written 13.0 years ago by
Ct586
▴ 620
83
votes
30
replies
6.8k
views
18 follow
Forum:
Optimal design for bioinformatics "lab" space?
design
lab-space
updated 22 months ago by
Ram
43k • written 9.0 years ago by
Casey Bergman
18k
1,000 results • Page
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Recent Votes
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
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Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
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Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
Lluís R.
★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers
by
christopher medway
▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
Comment: ChIP-seq datasets: input samples omitted?
by
i.sudbery
19k
Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
by
i.sudbery
19k
See the section on non full rank design matrices in the DESeq2 manual. In this case your problem is that healthy and 0dpi samples are e…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing?
by
jinyu
▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
Answer: Is it possible to bulk download files from GEO repository?
by
atharvakarkare14
▴ 10
Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
OK. Problem solved. The problem was from my end. Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
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