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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
103
votes
27
replies
88k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 10 months ago by
NIRJHAR
• 0 • written 11.8 years ago by
Rubal7
▴ 830
76
votes
26
replies
118k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 4 months ago by
cschu181
★ 2.8k • written 8.9 years ago by
Chenglin
▴ 260
21
votes
26
replies
9.4k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 14 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner
snp
sequencing
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
160k
20
votes
26
replies
3.1k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment
fasta
image
updated 7 months ago by
Joe
21k • written 4.8 years ago by
Joel Wallenius
▴ 210
33
votes
26
replies
3.5k
views
7 follow
Forum:
Poll: How many people have PyPy?
pypy
python
updated 11 months ago by
Ram
43k • written 8.1 years ago by
John
13k
3
votes
26
replies
1.8k
views
6 follow
STAR Genome index Error
STAR
updated 5 months ago by
Ram
43k • written 5 months ago by
Prasanna
• 0
47
votes
26
replies
4.0k
views
11 follow
Blog:
Evolution of Biostars
meta
Biostars
updated 7 months ago by
aldhairmedico
▴ 70 • written 5.1 years ago by
venu
7.1k
24
votes
26
replies
2.1k
views
6 follow
Forum:
Organizing a Bioinformatics Conference ?
meeting
conference
updated 10 months ago by
Ram
43k • written 6.4 years ago by
Pierre Lindenbaum
160k
105
votes
26
replies
42k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 6 months ago by
zx8754
11k • written 11.2 years ago by
henryvuong
▴ 810
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
User 59
13k
38
votes
26
replies
18k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.1 years ago by
biostart
▴ 370
24
votes
26
replies
3.5k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 9 months ago by
Ram
43k • written 4.4 years ago by
German.M.Demidov
★ 2.9k
7
votes
25
replies
10k
views
6 follow
Tool:
MIGEC: towards error-free profiling of immune repertoires
sequencing-error
tcr
antibody
molecular-barcode
updated 9 months ago by
Ram
43k • written 9.9 years ago by
mikhail.shugay
3.5k
69
votes
25
replies
6.9k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Dave Gerrard
▴ 190
39
votes
25
replies
4.3k
views
9 follow
Forum:
Making a mac book Bioinfo ready (El Capitan)
mac
software-installation
updated 11 months ago by
Ram
43k • written 8.1 years ago by
Eric Normandeau
11k
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 3 months ago by
asalimih
▴ 60 • written 9.6 years ago by
mike
▴ 90
11
votes
25
replies
6.1k
views
15 follow
News:
Questions for the NCBI Next Generation Sequencing Online Workshop Can be Posted with the NCBI_NOW Tag
NCBI_NOW
updated 12 months ago by
Ram
43k • written 8.5 years ago by
DCGenomics
▴ 330
13
votes
25
replies
4.2k
views
7 follow
VEP output has no gene names
alignment
sequencing
vep
updated 10 months ago by
barslmn
★ 2.1k • written 5.6 years ago by
Gene_MMP8
▴ 230
17
votes
25
replies
2.4k
views
Tool:
Platform for Bioinformatics Students, Scholars and Scientists
sequence
genome
updated 9 months ago by
Ram
43k • written 8.1 years ago by
support
▴ 50
6
votes
25
replies
38k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 10 months ago by
13554221497
• 0 • written 6.0 years ago by
ARich
▴ 130
51
votes
25
replies
6.8k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service
subjective
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Michael
54k
13
votes
25
replies
11k
views
9 follow
Tool:
Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis
sequencing
ngs
updated 9 months ago by
Ram
43k • written 10.6 years ago by
mikhail.shugay
3.5k
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general
subjective
updated 5 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
67
votes
25
replies
15k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 5 months ago by
GenoMax
140k • written 5.1 years ago by
Phil Ewels
★ 1.4k
59
votes
25
replies
5.2k
views
8 follow
Forum:
Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size
statistical-power
RNA-Seq
updated 9 months ago by
Ram
43k • written 3.6 years ago by
telroyjatter
▴ 220
18
votes
25
replies
14k
views
13 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 8 months ago by
Pierre Lindenbaum
160k • written 2.2 years ago by
ConvolutedGenome
▴ 20
38
votes
25
replies
9.0k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 6 months ago by
Ram
43k • written 8.0 years ago by
waqasnayab
▴ 250
64
votes
24
replies
2.9k
views
12 follow
Forum:
How much I must feel useless?
machine-learning
Programming
statistics
updated 10 months ago by
Ram
43k • written 5.5 years ago by
Molecular_genetics
▴ 80
159
votes
24
replies
62k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 9 months ago by
Ram
43k • written 11.1 years ago by
Nicolas Rosewick
10k
15
votes
24
replies
2.5k
views
7 follow
Forum:
Airport.bio: First class ticket to any biological database in the world
RNA-Seq
ChIP-Seq
SNP
updated 10 months ago by
Ram
43k • written 6.0 years ago by
Bohdan Khomtchouk
▴ 350
20
votes
24
replies
6.8k
views
6 follow
Forum:
Python or R
RNA-Seq
alignment
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 5.8 years ago by
Qingyang Xiao
▴ 160
27
votes
24
replies
2.4k
views
7 follow
Code Golf - bisulfite conversion
bisulfite
bsseq
code-golf
updated 10 months ago by
Ram
43k • written 5.5 years ago by
Chris Miller
22k
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 4 months ago by
Ram
43k • written 13.9 years ago by
Giovanni M Dall'Olio
28k
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
160k
21
votes
24
replies
3.2k
views
Forum:
From DEGs of a non-model animals to statistically significantly enriched pathways
pathway-enrichment
GO
RNA-Seq
KEGG
updated 11 months ago by
Ram
43k • written 7.6 years ago by
Farbod
★ 3.4k
48
votes
24
replies
8.1k
views
14 follow
Tool:
Hera: A new tool for RNA-Seq analysis
kallisto
RNA-Seq
STAR
gene-fusion
updated 9 months ago by
Ram
43k • written 6.7 years ago by
sonpham
▴ 580
4
votes
24
replies
5.9k
views
Split a concatenated alignment in multiple files
alignment
fasta
updated 5 months ago by
Felipe
• 0 • written 9.0 years ago by
dago
★ 2.8k
54
votes
24
replies
4.1k
views
12 follow
News:
Big news from Microsoft. BASH on windows.
windows
updated 11 months ago by
Ram
43k • written 8.0 years ago by
poisonAlien
★ 3.2k
14
votes
23
replies
2.7k
views
6 follow
Forum:
How can bioinformatics tools be grouped/divided into types?
sequencing
genome
updated 11 months ago by
Ram
43k • written 8.0 years ago by
harne.priyanka
▴ 110
33
votes
23
replies
21k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 6 months ago by
alejandrogzi
▴ 120 • written 6.0 years ago by
JJ
▴ 670
14
votes
23
replies
7.9k
views
6 follow
Calculate percentage of bases covered less than nX in targeted sequencing experiment
coverage
NGS
targeted sequencing
updated 11 months ago by
anii
• 0 • written 9.2 years ago by
Ram
43k
18
votes
23
replies
7.5k
views
7 follow
How to exclude some of breast cancer subtypes just by looking at gene expression?
RNA-Seq
genome
cancer
gene
updated 9 months ago by
Safu
• 0 • written 6.3 years ago by
jack
▴ 960
66
votes
23
replies
48k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 11 days ago by
Getnet Tesfaw
• 0 • written 6.3 years ago by
1769mkc
★ 1.2k
93
votes
23
replies
90k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 9 weeks ago by
clara.apicella
• 0 • written 5.7 years ago by
otwtgin2010
▴ 610
6
votes
23
replies
26k
views
6 follow
devtools Installation error in R (version 3.5.3)?
github
R
phylogeny
devtools
updated 10 months ago by
Ram
43k • written 5.0 years ago by
Kumar
▴ 120
56
votes
23
replies
4.9k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 9 months ago by
Ram
43k • written 7.7 years ago by
dariober
14k
11
votes
23
replies
1.6k
views
gatk Hardfilter Error
hardfilter
updated 10 months ago by
Michael
54k • written 10 months ago by
bestone
▴ 30
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp
amino-acids
updated 11 weeks ago by
gernophil
▴ 80 • written 12.2 years ago by
Preethi
▴ 110
33
votes
23
replies
3.9k
views
8 follow
Forum:
Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF
file-format
genomics
updated 9 months ago by
Jeremy Leipzig
22k • written 9 months ago by
LauferVA
4.1k
1,000 results • Page
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Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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104k
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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