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1,000 results • Page
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Votes
Replies
32
votes
51
replies
17k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq
samtools
bedtools
bam
updated 11.5 years ago by
brentp
24k • written 11.5 years ago by
User 9996
▴ 840
61
votes
51
replies
20k
views
9 follow
Tool:
Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
next-gen
sff
Tool
sequence
fastq
updated 18 months ago by
Ram
39k • written 9.1 years ago by
BioApps
▴ 790
179
votes
51
replies
15k
views
26 follow
I Am Preparing A Course On Ngs: Any Suggestion ?
next-gen
sequencing
galaxy
updated 9.9 years ago by
sarahhunter
▴ 600 • written 12.6 years ago by
Pierre Lindenbaum
154k
12
votes
50
replies
2.9k
views
How can I find out the Linux version and what is the ftp command to install R and R Studio on Linux server?
R
6.2 years ago by
thomas.f.hahn2
▴ 100
22
votes
50
replies
15k
views
Why I can not install anything on R?
R
software error
4.6 years ago by
Za
▴ 140
26
votes
50
replies
11k
views
8 follow
Tool:
Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta
multi-fasta
retrieval
large file
illumina
Tool
updated 7.0 years ago by
shenwei356
8.1k • written 7.0 years ago by
hcwang
▴ 50
188
votes
50
replies
68k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 8 months ago by
Ram
39k • written 12.6 years ago by
Zhangleisdau
▴ 340
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 3 months ago by
Ram
39k • written 8.1 years ago by
fhsantanna
▴ 610
93
votes
50
replies
14k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 3 months ago by
Ram
39k • written 9.5 years ago by
Istvan Albert
98k
262
votes
48
replies
21k
views
37 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 3 months ago by
Lars
▴ 970 • written 8.1 years ago by
Deepak Tanwar
★ 4.2k
72
votes
48
replies
7.1k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 3 months ago by
Ram
39k • written 12.1 years ago by
User 59
13k
68
votes
48
replies
7.1k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
updated 24 days ago by
Ram
39k • written 5.9 years ago by
Istvan Albert
98k
72
votes
48
replies
16k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 3 months ago by
Ram
39k • written 10.3 years ago by
lh3
33k
131
votes
48
replies
14k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 11.8 years ago by
Guangchuang Yu
★ 2.6k • written 11.8 years ago by
Eric Normandeau
11k
39
votes
48
replies
5.2k
views
CUTADAPT in windows
sequencing
updated 3 months ago by
Ram
39k • written 8.1 years ago by
fi1d18
★ 4.2k
22
votes
47
replies
4.0k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 4.2 years ago by
gb
★ 2.2k • written 4.7 years ago by
fishgolden
▴ 460
188
votes
47
replies
1.2k
views
16 follow
Job:
Bioinformatics freelancers needed
freelancer
updated 8 weeks ago by
Ram
39k • written 7.1 years ago by
Bioinfexperts
▴ 190
22
votes
47
replies
5.6k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 12.2 years ago by
Khader Shameer
18k • written 12.2 years ago by
Andrea_Bio
★ 2.8k
18
votes
47
replies
3.6k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
6.3 years ago by
dzisis1986
▴ 60
43
votes
46
replies
3.2k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 6.7 years ago by
Ram
39k • written 6.7 years ago by
fi1d18
★ 4.2k
92
votes
46
replies
10k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 3 months ago by
Ram
39k • written 11.9 years ago by
Andra Waagmeester
3.2k
37
votes
46
replies
5.6k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 4.7 years ago by
Ram
39k • written 13.1 years ago by
Jeremy Leipzig
21k
105
votes
46
replies
12k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 3 months ago by
Ram
39k • written 9.8 years ago by
ugly.betty77
★ 1.1k
125
votes
46
replies
44k
views
20 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization
ChIP-Seq
homer
ngsplot
deeptools
updated 8 weeks ago by
Ram
39k • written 7.2 years ago by
Sinji
★ 3.2k
20
votes
45
replies
11k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 4 months ago by
Ram
39k • written 8.1 years ago by
Ron
★ 1.1k
106
votes
45
replies
81k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 9 months ago by
aswinssoman
▴ 30 • written 10.9 years ago by
Mchimich
▴ 320
184
votes
45
replies
30k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
general
pipeline
updated 20 months ago by
Ram
39k • written 13.3 years ago by
Giovanni M Dall'Olio
27k
235
votes
45
replies
69k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 12.0 years ago by
User 9126
▴ 50 • written 13.0 years ago by
Biomed
4.9k
4
votes
45
replies
6.3k
views
SAM file wrong? help with validatesamfile
EXOME
updated 8 weeks ago by
Ram
39k • written 7.0 years ago by
cristina_sabiers
▴ 110
102
votes
44
replies
7.9k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 3 months ago by
Ram
39k • written 9.8 years ago by
brentp
24k
126
votes
44
replies
28k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 12 weeks ago by
Ram
39k • written 6.7 years ago by
Lars
▴ 970
90
votes
44
replies
58k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 13 months ago by
Ram
39k • written 12.1 years ago by
Ryan D
★ 3.4k
21
votes
44
replies
3.0k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
2.8 years ago by
Kumar
▴ 170
99
votes
44
replies
22k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text
r
perl
python
updated 5.8 years ago by
grant.hovhannisyan
★ 2.5k • written 11.2 years ago by
John
★ 1.5k
121
votes
44
replies
19k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 3 months ago by
Ram
39k • written 13.0 years ago by
Madelaine Gogol
5.3k
44
votes
44
replies
23k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 8 months ago by
Ram
39k • written 9.1 years ago by
Paul
★ 1.5k
152
votes
44
replies
29k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 11 months ago by
Ram
39k • written 9.4 years ago by
Carlos Borroto
★ 2.0k
25
votes
44
replies
12k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 9 months ago by
Ram
39k • written 7.6 years ago by
seta
★ 1.8k
196
votes
44
replies
69k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 4 months ago by
Ram
39k • written 10.7 years ago by
Obi Griffith
20k
66
votes
43
replies
25k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen
sequencing
parsing
fastq
programming
updated 16 months ago by
Ram
39k • written 12.4 years ago by
toni
★ 2.2k
19
votes
43
replies
4.2k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.8 years ago by
nazaninhoseinkhan
▴ 510
1
vote
43
replies
2.5k
views
Database from .gbk files
database
gbk
ncbi
updated 7 weeks ago by
Raul
• 0 • written 3.0 years ago by
graysonford
▴ 10
57
votes
43
replies
14k
views
8 follow
Forum:
Best RNA-Seq aligner: A comparison of mapping tools
NGS
alignment
genome
RNA-Seq
sequence
updated 12 weeks ago by
Ram
39k • written 4.4 years ago by
David Langenberger
9.9k
185
votes
43
replies
79k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 9 months ago by
Ram
39k • written 13.2 years ago by
Yuri
★ 1.6k
170
votes
43
replies
16k
views
25 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
updated 5 weeks ago by
zx8754
11k • written 10.2 years ago by
Istvan Albert
98k
31
votes
43
replies
17k
views
11 follow
Volcano plot help code
R
rna-seq
updated 5.0 years ago by
jordi.planells
▴ 450 • written 5.1 years ago by
anasofiamoreira94
▴ 80
16
votes
43
replies
5.6k
views
Stuck on calculating principal components
Vegan
R
software error
SNP
updated 5.5 years ago by
pfs
▴ 280 • written 5.5 years ago by
fi1d18
★ 4.2k
59
votes
43
replies
19k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 11 weeks ago by
Ram
39k • written 5.7 years ago by
Rox
★ 1.4k
138
votes
42
replies
20k
views
22 follow
Forum:
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 10 weeks ago by
Vincent Laufer
★ 2.9k • written 10.0 years ago by
Whetting
★ 1.6k
28
votes
42
replies
5.6k
views
7 follow
How to add tophat and bowtie to the path?
export PATH
bowtie2.2.9
tophat2
6.5 years ago by
mirza
▴ 180
1,000 results • Page
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Recent Votes
Comment: Italicise annotations with pheatmap
Visualizing Graph Alignment Format via minigraph
Gene prediction software
ClusterProfiler : What is GeneRatio and BgRatio?
ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
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Recent Replies
Comment: Stratified sample assignment for analysis
by
ATpoint
72k
Batches for what? Processing/sequencing, what data are we talking about? If this is indeed paired then you basically must keep samples of a…
Answer: Visualizing Graph Alignment Format via minigraph
by
colindaven
4.8k
That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like forma…
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
BTW - Most TCGA cancer types do have normals amoungst the samples.
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
The assumption of these studies is that any batch effect within a batch affects both treatment and control equally, so that when you divide…
Answer: Stratified sample assignment for analysis
by
Vincent Laufer
★ 2.9k
First, you didn't tell us what kind of data you are working with. For arguments sake, I'll assume bulk RNA-seq. Generally, your options …
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★ 2.2k
You can use the ---show_ref_allele flag when running the VEP query. This will add the reference allele in the output and is mainly useful f…
Comment: Get relationships and hierarchies for GO terms
by
Alexander
▴ 70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Alexander
▴ 70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments. I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use?
by
fracarb8
▴ 950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software
by
alexandru.bologa.marian
▴ 40
Hi, I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
▴ 60
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
Yes, that is what methylkit is for. See my answer.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
Inkscape you learn in a day, for basic image and figure manipulation it's really simple and a good skill to have. Highly recommended.
Comment: Installation of PPFinder
by
subashini.fbtpb106
▴ 10
Can you suggest me any software that does gene prediction by masking pseudogenes?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
IMHO this is like asking for the cow when you only have a steak :-)
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