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117,087 results • Page
5 of 2342
Sort: Votes
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Views
Votes
Replies
81
votes
21
replies
5.1k
views
16 follow
Forum:
[UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 14 months ago by
Ram
44k • written 7.9 years ago by
Sinji
★ 3.2k
81
votes
6
replies
46k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam
samtools
next-gen
updated 2.2 years ago by
Ram
44k • written 12.1 years ago by
Stefano Berri
4.4k
81
votes
21
replies
43k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 8 months ago by
Joel Wallenius
▴ 210 • written 10.3 years ago by
pristanna
▴ 750
81
votes
4
replies
21k
views
Discrimination Between Germline And Somatic Mutations In Tumor Without The Availability Of The Normal Paired Sample
mutation
somatic
updated 11.2 years ago by
Stefano Berri
4.4k • written 11.2 years ago by
Fred Fleche
4.3k
81
votes
23
replies
12k
views
10 follow
Transform A Pipeline Of R Scripts Into A Web Application
webservice
web
pipeline
galaxy
updated 2.1 years ago by
Ram
44k • written 13.8 years ago by
Giovanni M Dall'Olio
28k
81
votes
22
replies
92k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen
sequencing
fasta
rna
r
perl
updated 18 months ago by
Ram
44k • written 12.6 years ago by
Hamilton
▴ 290
81
votes
15
replies
24k
views
10 follow
Vertebrate Subset Nr Database? Build My Own?
blast
database
updated 9.9 years ago by
jcsoellner
• 0 • written 13.2 years ago by
Jason
▴ 430
81
votes
39
replies
7.7k
views
11 follow
News:
State Of Biostar - Future Directions (January 2013)
biostars
updated 15 months ago by
Ram
44k • written 11.4 years ago by
Istvan Albert
100k
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 7 months ago by
Ram
44k • written 14.2 years ago by
User 59
13k
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 6 months ago by
Ram
44k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
80
votes
21
replies
37k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 6 months ago by
kathryn.jacksonjones
• 0 • written 10.1 years ago by
M K
▴ 660
80
votes
27
replies
56k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 21 months ago by
Johan Zicola
▴ 70 • written 10.4 years ago by
Ram
▴ 190
80
votes
34
replies
5.4k
views
11 follow
Forum:
Authorship issues- how to resolve?
authorship
updated 16 months ago by
Ram
44k • written 9.0 years ago by
datanerd
▴ 520
80
votes
23
replies
5.3k
views
11 follow
Forum:
Are we facing a bioinformatician shortage?
salary
career
updated 14 months ago by
Ram
44k • written 9.6 years ago by
Christian
★ 3.0k
79
votes
16
replies
48k
views
11 follow
How do you cite a tool that doesn't have a publication?
citation
academic
style
updated 8.1 years ago by
Emily
23k • written 8.2 years ago by
novice
★ 1.1k
79
votes
86
replies
32k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 11 months ago by
Ram
44k • written 7.5 years ago by
Brian Bushnell
20k
79
votes
35
replies
9.8k
views
17 follow
Forum:
Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship
career
updated 12 months ago by
jli.ww
• 0 • written 8.5 years ago by
sentausa
▴ 650
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 11 weeks ago by
nickp60
▴ 60 • written 7.9 years ago by
andrew.j.skelton73
6.6k
78
votes
31
replies
6.9k
views
14 follow
Forum:
Do Bad Questions Even Exist?
biostars
general
education
updated 15 months ago by
Ram
44k • written 13.2 years ago by
Chris Evelo
10k
78
votes
12
replies
39k
views
8 follow
How Can I Get The Human Chromosome Centromere Position And Chromosome Length In Grch37/Hg19
position
ucsc
updated 5.5 years ago by
Shixiang
▴ 100 • written 13.7 years ago by
Jdk
▴ 260
77
votes
9
replies
13k
views
15 follow
Which program, tool, or strategy do you use to visualize genomic rearrangements?
fusion-genes
visualizations
rearrangements
updated 20 months ago by
Ram
44k • written 8.7 years ago by
stianlagstad
★ 1.1k
77
votes
26
replies
121k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 6 months ago by
cschu181
★ 2.8k • written 9.1 years ago by
Chenglin
▴ 260
77
votes
13
replies
16k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 2.6 years ago by
Ram
44k • written 10.0 years ago by
Malachi Griffith
20k
77
votes
24
replies
61k
views
16 follow
How To Sort Bed Format File
bed
updated 19 months ago by
Pierre Lindenbaum
162k • written 11.2 years ago by
lyz10302012
▴ 450
77
votes
22
replies
23k
views
14 follow
Assessing The Quality Of De Novo Assembled Data
assembly
next-gen
updated 20 months ago by
Ram
44k • written 11.9 years ago by
Prakki Rama
★ 2.7k
77
votes
15
replies
10k
views
10 follow
Best Bioinformatics Research Images
visualization
updated 12.8 years ago by
Simon Cockell
7.4k • written 12.9 years ago by
Niallhaslam
2.3k
77
votes
10
replies
21k
views
6 follow
what do the headers of the rMATS output files mean?
MATS
Alternative splicing
next-gen
STAR
updated 5.5 years ago by
drskm7
• 0 • written 7.0 years ago by
atcggcta
▴ 140
77
votes
11
replies
33k
views
9 follow
Star Or Tophat?
rnaseq
alignment
tophat
updated 3.1 years ago by
Ram
44k • written 10.4 years ago by
lkmklsmn
▴ 970
77
votes
20
replies
15k
views
12 follow
Perl Or Python For Comparative Genomics?
bioperl
biopython
python
comparative
updated 6.0 years ago by
lakhujanivijay
5.8k • written 13.6 years ago by
Dave Lunt
★ 2.0k
77
votes
18
replies
46k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 22 months ago by
Dan
• 0 • written 14.0 years ago by
Science_Robot
★ 1.1k
77
votes
16
replies
34k
views
14 follow
Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier
genbank
conversion
ncbi
taxonomy
updated 7.3 years ago by
-_-
★ 1.1k • written 12.8 years ago by
Alf
▴ 490
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
27 days ago by
Kevin Blighe
88k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 11 months ago by
Ram
44k • written 7.0 years ago by
bernatgel
★ 3.4k
76
votes
22
replies
54k
views
17 follow
How To Download All Sra Samples At Once ?
geo
sra
updated 14 months ago by
Ram
44k • written 10.3 years ago by
biorepine
★ 1.5k
76
votes
24
replies
21k
views
18 follow
What Methods Do You Use For Short Read Mapping?
short-read-aligner
sequence
updated 4.8 years ago by
Ram
44k • written 14.2 years ago by
Biostar User
★ 1.0k
76
votes
14
replies
16k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 15 months ago by
Ram
44k • written 11.0 years ago by
Medhat
9.7k
75
votes
19
replies
3.6k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 11 weeks ago by
LauferVA
4.2k • written 8 months ago by
Kenny
▴ 30
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing
duplicates
updated 6 months ago by
Ram
44k • written 14.1 years ago by
Pierre Lindenbaum
162k
75
votes
3
replies
39k
views
Tutorial:
Revisiting the FastQC read duplication report
fastqc
updated 2.5 years ago by
Ram
44k • written 9.8 years ago by
Istvan Albert
100k
75
votes
13
replies
67k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 18 months ago by
Ram
44k • written 10.5 years ago by
Nicholas Spies
★ 1.2k
74
votes
14
replies
30k
views
12 follow
Forum:
Bioinformatics Consulting Thoughts
consulting
updated 23 months ago by
Ram
44k • written 13.9 years ago by
Will
4.5k
74
votes
16
replies
4.8k
views
10 follow
Tools & Techniques Bioinformatician Have To Master?
subjective
updated 10 months ago by
Ram
44k • written 13.2 years ago by
Thaman
★ 3.3k
73
votes
14
replies
4.3k
views
12 follow
Forum:
Things you wish you knew when entering the bioinformatics field
pitfalls
advice
updated 11 months ago by
Ram
44k • written 3.7 years ago by
jared.andrews07
★ 17k
73
votes
60
replies
28k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 15 months ago by
Ram
44k • written 6.7 years ago by
Kevin Blighe
88k
73
votes
7
replies
13k
views
6 follow
What Should I Use Blat For?
alignment
updated 11.5 years ago by
David Quigley
11k • written 11.5 years ago by
KCC
★ 4.1k
73
votes
25
replies
9.1k
views
16 follow
The Five Most Annoying Bioinformatics Problems You Face Every Week?
updated 10.7 years ago by
Mary
11k • written 10.7 years ago by
davidcassali
▴ 60
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by
snardeli
• 0 • written 10.3 years ago by
Istvan Albert
100k
72
votes
18
replies
7.5k
views
17 follow
Forum:
What Is One Book Every Bioinformatician Should Read?
books
updated 15 months ago by
Ram
44k • written 10.9 years ago by
Philipp Bayer
8.5k
72
votes
20
replies
26k
views
11 follow
Parsing Ncbi Taxonomic Tree?
ncbi
taxonomy
python
tree
updated 17 months ago by
Ram
44k • written 12.6 years ago by
Prohan
▴ 350
72
votes
15
replies
20k
views
12 follow
Counting N'S Within Fasta
fasta
counts
perl
updated 6.0 years ago by
Biostar
20 • written 12.1 years ago by
PoGibas
5.1k
117,087 results • Page
5 of 2342
Recent Votes
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
C: Reads mapped to another chromosome in paired-end data of RNA-seq
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Recent Replies
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
bk11
★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files
by
a.penatauber
• 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq
by
ATpoint
82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP
by
Pierre Lindenbaum
162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
Answer: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> have two bed files these are not bed files. A chromosome is missing in chromosome 1 > How can I create a file from the two mention…
Comment: Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
by
GenoMax
142k
Have you checked for presence of rRNA in the affected samples? That can be one possibility for these peaks. In theory if you are aligning …
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Comment: Trimmomatic running but files containing purged reads are empty
by
GenoMax
142k
Perhaps there were no low quality reads either.
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Arton
▴ 10
Thank you for the helpful answer!
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
DBScan
▴ 300
I think GATK only counts informative reads in AD, do you have a DP field? DP should be closer what FreeBayes reports. You can also check GA…
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