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1,000 results • Page
4 of 20
Sort: Votes
Rank
Views
Votes
Replies
44
votes
3
replies
13k
views
Tutorial:
A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics
computational-biology
updated 11 months ago by
Ram
43k • written 8.0 years ago by
Sinji
★ 3.2k
44
votes
9
replies
5.3k
views
6 follow
How Much Do You Trust Geneontology Annotations?
gene-function
subjective
updated 5 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
44
votes
9
replies
57k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen
RNA-Seq
single-cell
R
updated 7 months ago by
camillab.
▴ 160 • written 4.3 years ago by
Payal
▴ 160
44
votes
4
replies
20k
views
Best way to compare two samples in a VCF file
VCF
Variant
Genotype
Comparison
SNP
updated 7 months ago by
Ram
43k • written 7.3 years ago by
Matteo Schiavinato
★ 3.6k
43
votes
12
replies
5.7k
views
11 follow
What Is The Best Way To Share Scripts Between Members Of A Lab?
general
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
43
votes
37
replies
2.4k
views
7 follow
Forum:
Checking the quality and reliability in bioinformatics
reproducibility
updated 10 months ago by
Ram
43k • written 6.5 years ago by
zizigolu
★ 4.3k
43
votes
44
replies
5.4k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics
amplicon
macbook
Intel
MacOs
updated 5 months ago by
steve
★ 3.5k • written 5 months ago by
l.gallucci
▴ 10
43
votes
28
replies
5.5k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
43
votes
21
replies
5.4k
views
9 follow
Helping Biostar Grow
biostars
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
42
votes
16
replies
33k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 6 months ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
chparada
▴ 70
42
votes
15
replies
12k
views
12 follow
Preferred Tools For Making Analysis Pipeline Flowchart ?
pipeline
updated 9 months ago by
Ram
43k • written 11.1 years ago by
VS
▴ 730
42
votes
20
replies
3.3k
views
11 follow
Forum:
What are the most popular NGS tools?
ensembl
NGS
updated 11 months ago by
Ram
43k • written 8.0 years ago by
Emily
23k
41
votes
27
replies
5.9k
views
8 follow
Forum:
Why bioinformaticians need to know programming languages?
Python
R
Programming
updated 10 months ago by
Ram
43k • written 6.8 years ago by
nilo
▴ 90
41
votes
13
replies
25k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 20 days ago by
CTLong
▴ 90 • written 6.4 years ago by
Sreeraj Thamban
▴ 290
40
votes
6
replies
15k
views
7 follow
Mapping Ensembl Gene IDs with dot suffix
ensembl
gene
biomart
bioconductor
R
updated 8 months ago by
zx8754
11k • written 6.1 years ago by
mk
▴ 290
40
votes
35
replies
13k
views
10 follow
find positions of a short sequence in a genome
sequence
search
updated 7 months ago by
Mark
★ 1.5k • written 7.6 years ago by
igor
13k
40
votes
23
replies
4.0k
views
12 follow
Forum:
Why learn programming in bioinformatics?
Programming
updated 10 months ago by
Ram
43k • written 5.6 years ago by
joselu
▴ 110
40
votes
19
replies
9.5k
views
12 follow
Is There A Site Where Call For Papers And Conferences Are Listed In One Place?
papers
conference
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Brandstaetter
▴ 270
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 10 months ago by
Ram
43k • written 6.6 years ago by
steve
★ 3.5k
39
votes
15
replies
23k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene
r
updated 4 months ago by
Ram
43k • written 14.0 years ago by
John
▴ 790
39
votes
21
replies
13k
views
10 follow
Forum:
Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.4 years ago by
Juke34
8.5k
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
39
votes
11
replies
8.9k
views
11 follow
Where Can I Get The Secondary Structure Of A Protein?
protein
structure
sequence
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
39
votes
28
replies
10k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
8 weeks ago by
Jeremy Leipzig
22k
39
votes
18
replies
5.9k
views
10 follow
Any Open Notebook Science In Bioinformatics?
open-notebook
updated 4 months ago by
Ram
43k • written 13.9 years ago by
Heather Piwowar
▴ 380
39
votes
23
replies
33k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 6 months ago by
s.w.vanderlaan
▴ 40 • written 2.7 years ago by
Michal Nevo
▴ 130
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
140k • written 3.6 years ago by
lavinia.gordon
▴ 160
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 9 months ago by
Ram
43k • written 8.0 years ago by
John
13k
38
votes
11
replies
4.0k
views
7 follow
Python Documentation Tools
python
updated 9 months ago by
Ram
43k • written 13.8 years ago by
Thaman
★ 3.3k
38
votes
14
replies
9.0k
views
8 follow
Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
ensembl
python
biopython
genome
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Rvidal
▴ 270
38
votes
19
replies
10k
views
10 follow
Forum:
Kallisto New RNA-seq quantification method discussion
RNA-Seq
updated 11 months ago by
Ram
43k • written 8.0 years ago by
morovatunc
▴ 550
38
votes
8
replies
1.5k
views
6 follow
News:
What happens when a bioinformatician has his own genome sequenced for $300?
DNAseq
DNA
WGS
updated 9 months ago by
Alex Reynolds
35k • written 9 months ago by
David Langenberger
11k
38
votes
17
replies
3.1k
views
7 follow
Forum:
Why does bioinformatics use a special format like a BAM file instead of a database like SQLite?
sam
bam
samtools
updated 9 months ago by
Ram
43k • written 3.6 years ago by
kojix2
▴ 250
38
votes
31
replies
2.8k
views
10 follow
Forum:
To the Biologists out there: What bioinf tool are you missing?
education
career
updated 11 months ago by
Ram
43k • written 7.7 years ago by
mschmid
▴ 180
38
votes
7
replies
2.2k
views
News:
2 last seats available - 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Transcriptomics
DNA-Seq
Variant-Calling
RNA-Seq
8 months ago by
David Langenberger
11k
38
votes
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed
ensembl
bedops
gtf
updated 4 weeks ago by
Alex Reynolds
35k • written 7.6 years ago by
bioinformatics.cancer
▴ 260
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
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
38
votes
19
replies
11k
views
Tool:
Excel add-in for DNA/RNA string manipulations
sequence
DNA
RNA
Excel
updated 9 months ago by
Ram
43k • written 8.1 years ago by
jgbaum
▴ 140
37
votes
9
replies
4.3k
views
8 follow
What are the advantages of using the T2T as a reference vs GRCh38 today?
reference
GRCh38
t2t
calling
variant
updated 10 months ago by
LauferVA
4.1k • written 11 months ago by
onter
▴ 170
37
votes
20
replies
7.1k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
37
votes
16
replies
3.9k
views
9 follow
Forum:
Sanger sequencing is no longer the gold standard?
Sanger
NGS
updated 10 months ago by
Ram
43k • written 6.4 years ago by
lamteva.vera
▴ 220
36
votes
16
replies
14k
views
8 follow
How to identify 16s sequences from binning data(contigs)?
genome
Assembly
sequence
blast
updated 8 months ago by
Kermit
▴ 90 • written 8.5 years ago by
liuyifan2014
▴ 110
36
votes
17
replies
3.6k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Giovanni M Dall'Olio
28k
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
36
votes
8
replies
3.6k
views
6 follow
Forum:
Time Management Strategies and Advice for Bioinformaticians
professional-skills
updated 11 months ago by
Ram
43k • written 7.8 years ago by
sviatoslav.kendall
▴ 880
36
votes
11
replies
32k
views
6 follow
Sjdboverhang Option In Star
updated 8 months ago by
Kermit
▴ 90 • written 10.1 years ago by
Martombo
★ 3.1k
36
votes
39
replies
4.0k
views
11 follow
Forum:
Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast
RNA-Seq
alignment
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.4 years ago by
dhbradshaw
▴ 130
36
votes
13
replies
7.2k
views
8 follow
How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
data
galaxy
written 12.9 years ago by
Pi
▴ 520
36
votes
34
replies
2.7k
views
9 follow
Forum:
New to bioinformatics.....
gene
updated 10 months ago by
Ram
43k • written 6.0 years ago by
sms.00196
• 0
1,000 results • Page
4 of 20
Recent Votes
Which human reference genome should I use?
Comment: Centromere and telomere positions for Chm13v2 assembly
C: Last column in UCSC cytoBands.txt files
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
Comment: Gene reads all zero for each sample
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Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Looks like those appear to be "polycomb associated non-coding RNA". You probably know what they are. https://www.ncbi.nlm.nih.gov/nuccore/…
Comment: Parsing fasta file by coordinates
by
GenoMax
140k
> sequences that are from the same region from those that aren't. could refer to sequence composition and that is the reason we were sugge…
Comment: Low number of both surviving reads after trimming
by
Ram
43k
Please edit your post and add the code parts again, this time use the `101010` code button and NOT the double quote button. The latter is u…
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Pierre Lindenbaum
160k
... reminds me [https://twitter.com/yokofakun/status/1267877851795259397][1] ( my twitter account is now private) ![ops][2] [1]: https…
Comment: Flow Cytometry Data Analysis by Seurat
by
Ram
43k
Why did you delete this post, https://www.biostars.org/u/142036/ ?
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
dariober
14k
Perhaps more concerning is why you have features (genes?) with small pvalue but fold-change very close to zero. It's also unusual that ther…
Comment: Gene reads all zero for each sample
by
DYLAN NICO
• 0
Thank you for the suggestions. Unfortunately I cannot add any details for lack of information. But I will try using a different alignment a…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
They are +ve and -ve strands, but identical two by two ... I can filter that out later on. This is probably a very naive question, but what…
Comment: Gene reads all zero for each sample
by
ATpoint
81k
Do I understand correctly that you have one gene you are interested in, but all counts are zero, right? If so, first thing could be to use …
Answer: ONT direct RNA sequencing
by
joe
▴ 470
You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you !!
Answer: Can I have multiple active GDC download tokens?
by
Zhenyu Zhang
★ 1.1k
You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
Comment: Parsing fasta file by coordinates
by
sorrymouse
▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
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