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1,000 results • Page
4 of 20
Sort: Votes
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Views
Votes
Replies
33
votes
26
replies
3.6k
views
7 follow
Forum:
Poll: How many people have PyPy?
pypy
python
updated 13 months ago by
Ram
43k • written 8.2 years ago by
John
13k
33
votes
5
replies
16k
views
9 follow
Forum:
How do I explain to my non-bioinformatician labmates how to interpret principal components?
RNA-Seq
communication
analysis
pca
updated 21 months ago by
Ram
43k • written 8.4 years ago by
Kristin Muench
▴ 620
33
votes
23
replies
4.3k
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 11 months ago by
Jeremy Leipzig
22k • written 11 months ago by
LauferVA
4.2k
32
votes
13
replies
11k
views
10 follow
Forum:
What Skills Do You Have To Have As A Phd Graduate In Bioinformatics?
genomics
phd
updated 14 months ago by
Ram
43k • written 11.8 years ago by
sentausa
▴ 650
32
votes
5
replies
5.6k
views
Forum:
ipython notebooks on bioinformatics and genomics
python
updated 13 months ago by
Ram
43k • written 8.9 years ago by
Pappu
★ 2.1k
32
votes
16
replies
12k
views
9 follow
Forum:
How to switch from bench research to computational biology?
career
updated 22 months ago by
Ram
43k • written 9.2 years ago by
yuggnurug
▴ 70
32
votes
14
replies
6.8k
views
9 follow
Forum:
Pat Schloss of Mothur uses this
uses-this
updated 14 months ago by
Ram
43k • written 9.5 years ago by
Istvan Albert
100k
32
votes
9
replies
5.9k
views
Forum:
Embrace The Non-Googlers Of Biostars
meta
biostars
updated 15 months ago by
Ram
43k • written 10.9 years ago by
KCC
★ 4.1k
31
votes
13
replies
16k
views
8 follow
Forum:
Should I Pursue A Bioinformatics Msc?
career
updated 14 months ago by
Ram
43k • written 11.3 years ago by
biostepho
▴ 70
31
votes
16
replies
2.2k
views
8 follow
Forum:
What is in your opinion the current state-of-the-art sequencing platform for genomic assembly (Nov 2019)
next-gen-sequencing
assembly
genome
updated 11 months ago by
Ram
43k • written 4.5 years ago by
Antonio R. Franco
★ 5.1k
31
votes
34
replies
7.5k
views
11 follow
Forum:
pros- and cons- : programming skills vs. GUI
programming
lecture
updated 13 months ago by
Ram
43k • written 8.5 years ago by
TriS
★ 4.7k
31
votes
41
replies
2.7k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 11 months ago by
Ram
43k • written 4.2 years ago by
K.Gee
▴ 40
31
votes
8
replies
3.8k
views
6 follow
Forum:
Getting Things Done In Bioinformatics (More I Know, Less I Do?)
literature
analysis
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Biomonika (Noolean)
3.2k
31
votes
7
replies
6.0k
views
9 follow
Forum:
Beginner in Bioinformatics / computational biology field
Bioinformatics
Computational-biology
updated 13 months ago by
Ram
43k • written 7.9 years ago by
tanvi.phaltane
▴ 70
31
votes
4
replies
5.6k
views
8 follow
Forum:
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2016?
Assembly
sequencing
RNA-Seq
updated 13 months ago by
Ram
43k • written 7.4 years ago by
dago
★ 2.8k
30
votes
5
replies
4.1k
views
Forum:
I'm applying for a non-PhD bioinformatics position in your lab. What do you look for?
sequencing
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
scical
▴ 100
30
votes
31
replies
3.8k
views
11 follow
Forum:
I need your help to find my future
internship
masters
career
updated 13 months ago by
Ram
43k • written 7.8 years ago by
Baptiste
▴ 90
30
votes
19
replies
10k
views
6 follow
Forum:
Programming language use distribution from recent programs / articles
programming-language
programs
updated 12 months ago by
Ram
43k • written 7.0 years ago by
Eric Normandeau
11k
30
votes
13
replies
3.7k
views
11 follow
Forum:
what is your daily must see bioinformatics web site?
learn
technology
updated 11 months ago by
Ram
43k • written 9.7 years ago by
Medhat
9.7k
30
votes
27
replies
2.6k
views
11 follow
Forum:
How do you spend your time (productively) when your script is running?
time-management
updated 13 months ago by
Ram
43k • written 7.3 years ago by
venu
7.1k
30
votes
16
replies
2.3k
views
9 follow
Forum:
Which programming langauge shall I start as a beginner in Bioinformatics
programming-language
single-cell
updated 11 months ago by
Ram
43k • written 4.1 years ago by
nkg.bb
• 0
29
votes
17
replies
2.3k
views
6 follow
Forum:
Can Biostars use question template like Github issue/PR?
meta
biostars
template
updated 13 months ago by
Ram
43k • written 7.2 years ago by
shenwei356
8.5k
29
votes
4
replies
7.9k
views
Forum:
Update to tbb (2021.1.1, conda-forge) breaks bowtie2 (bioconda)
software-error
bowtie2
bioconda
conda
tbb
updated 14 months ago by
Ram
43k • written 3.2 years ago by
mlbendall
▴ 240
29
votes
16
replies
3.2k
views
Forum:
Making bioinformatics help and tutorials open
ensembl
updated 14 months ago by
Ram
43k • written 9.8 years ago by
Emily
23k
29
votes
21
replies
6.3k
views
Forum:
PhD vs Field application scientist in industry
career
updated 13 months ago by
Ram
43k • written 7.8 years ago by
Govi988
▴ 80
29
votes
10
replies
6.5k
views
10 follow
Forum:
Interesting/useful/beautiful bio sequence viz tools
viz
python
visualisation
updated 14 months ago by
Ram
43k • written 6.2 years ago by
Joe
21k
29
votes
10
replies
3.2k
views
Forum:
How do you perform functional testing for your Bioinformatics tools?
development
testing
bug
reliability
updated 12 months ago by
Ram
43k • written 7.2 years ago by
shenwei356
8.5k
29
votes
4
replies
6.9k
views
Forum:
Biostar Vs. Seqanswers: What Is The Difference?
biostars
updated 15 months ago by
Ram
43k • written 11.0 years ago by
jobinv
★ 1.1k
29
votes
18
replies
2.7k
views
12 follow
Forum:
what are the big questions in bioinformatics field nowadays
genome
updated 11 months ago by
Ram
43k • written 4.2 years ago by
t4192
▴ 20
29
votes
10
replies
9.3k
views
Forum:
Principles of Tidy Data (Hadley Wickham) and the VCF format
vcf
tidy-data
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Giovanni M Dall'Olio
28k
29
votes
18
replies
3.3k
views
7 follow
Forum:
Should I quit PhD program?
education
career
research
phd
updated 11 months ago by
Ram
43k • written 6.0 years ago by
George
▴ 30
29
votes
13
replies
3.7k
views
6 follow
Forum:
Map of bioinformatics or who is bioinformatician.
self-study
updated 13 months ago by
Ram
43k • written 7.5 years ago by
dshulgin
▴ 260
28
votes
7
replies
5.3k
views
Forum:
Open Source projects to contribute to
contribute
open-source
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
shane
▴ 90
28
votes
14
replies
8.4k
views
8 follow
Forum:
Should I work first in a Bioinformatics company or get a Ph. D.?
Biochemistry
PhD
career
updated 13 months ago by
Ram
43k • written 8.0 years ago by
mvasquez16
▴ 20
28
votes
15
replies
2.3k
views
12 follow
Forum:
Should bioinformaticians learn the scientific names of plants and animals?
sequence
updated 11 months ago by
Ram
43k • written 5.9 years ago by
ivan.radonov
▴ 10
28
votes
13
replies
2.7k
views
Forum:
Are there any workshops which are tailored to non-beginners/intermediate bioinformatics?
workshop
updated 19 months ago by
Ram
43k • written 8.8 years ago by
Daniel
★ 4.0k
28
votes
14
replies
6.9k
views
9 follow
Forum:
How Do You Use Cloud Computing For Bioinformatics In 2013?
cloud
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Eric Normandeau
11k
28
votes
13
replies
1.5k
views
6 follow
Forum:
Suppose you have a sequencer that can read the genome end-to-end. What aspects of bioinformatics will become irrelevant?
future
updated 17 months ago by
Ram
43k • written 7.6 years ago by
Ayaan
▴ 40
28
votes
11
replies
3.2k
views
9 follow
Forum:
Getting started with NGS analysis, common issues?
software-error
next-gen
updated 2.1 years ago by
Ram
43k • written 9.2 years ago by
Keith
▴ 50
28
votes
7
replies
1.9k
views
Forum:
Do you have favorite icons for bioinformatics?
ubuntu
updated 14 months ago by
Ram
43k • written 3.2 years ago by
kojix2
▴ 250
28
votes
1
reply
6.9k
views
Forum:
Bedops: The Fastest, Most Scalable, And Easily-Parallelizable Genome Analysis Toolkit!
bedops
genome-analysis
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Alex Reynolds
35k
28
votes
31
replies
5.8k
views
8 follow
Forum:
Biostar Ads Are Now Live. Feedback And Comments Are Sought.
biostars
updated 15 months ago by
Ram
43k • written 10.9 years ago by
Istvan Albert
100k
28
votes
15
replies
4.5k
views
8 follow
Forum:
Anyone Use R For Their Bioinformatics Work?
r
updated 14 months ago by
Ram
43k • written 10.6 years ago by
arronslacey
▴ 320
27
votes
33
replies
3.8k
views
7 follow
Forum:
Biostars question catagories
statistics
biostars
meta
updated 13 months ago by
Ram
43k • written 7.6 years ago by
John
13k
27
votes
21
replies
9.3k
views
9 follow
Forum:
Better for my career: Degree in computer science or Phd in bioinformatics?
computer-science
phd
updated 13 months ago by
Ram
43k • written 7.7 years ago by
BioinfGuru
★ 1.7k
27
votes
11
replies
3.8k
views
10 follow
Forum:
Which programming language to integrate several open source software into one working pipeline (software)
MEGA
pipeline
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
benjamin.hebisch
▴ 70
27
votes
0
replies
8.1k
views
Forum:
Heng Li of BWA and Samtools uses this
uses-this
updated 14 months ago by
Ram
43k • written 9.6 years ago by
Istvan Albert
100k
27
votes
17
replies
5.1k
views
Forum:
Data sharing via Bittorrent is coming to Biostar
biostars
bittorrent
updated 15 months ago by
Ram
43k • written 9.8 years ago by
Istvan Albert
100k
27
votes
8
replies
4.8k
views
6 follow
Forum:
PhD in Bioinformatics: to continue, or not to continue? That is the question--
career
updated 14 months ago by
Ram
43k • written 10.0 years ago by
MAPK
★ 2.1k
27
votes
19
replies
4.6k
views
10 follow
Forum:
Google genomics cloud platform ?
genome
cloud
updated 14 months ago by
Ram
43k • written 8.9 years ago by
GouthamAtla
12k
1,000 results • Page
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Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
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Recent Replies
Answer: Annotating file using bcftools
by
Pierre Lindenbaum
161k
I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
I had the same problem in this iusse [https://github.com/nanoporetech/dorado/issues/603][1] and I solved it as they say here [1]: https…
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ATpoint
82k
Looking at this briefly, it is small sample size and you do not correct for any potential confounders. Use PCA or MDS to explore the data. …
Comment: bbmerge (bbmap) ~ error with insert size file output
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142k
> It is confirmed (and solved in another thread) that we have significant overlapping paired end reads. Can you provide a reference to sai…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
> I get the exact same read with the same ID and all more than once If you have short(er) reads you could be seeing secondary alignments. …
Answer: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data
by
Esraa
• 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data
by
i.sudbery
19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data
by
Esraa
• 0
**My references** Genome: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_al…
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
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ATpoint
82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis
by
Jacek
▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
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14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python
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JACKY
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I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
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