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13,539 results • Page
2 of 271
Sort: replies
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Views
Votes
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40
votes
35
replies
13k
views
10 follow
find positions of a short sequence in a genome
sequence
search
updated 8 months ago by
Mark
★ 1.5k • written 7.7 years ago by
igor
13k
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.9 years ago by
egeulgen
★ 1.3k
36
votes
34
replies
2.8k
views
9 follow
Forum:
New to bioinformatics.....
gene
updated 11 months ago by
Ram
43k • written 6.1 years ago by
sms.00196
• 0
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 8 weeks ago by
barslmn
★ 2.1k • written 6.7 years ago by
a.rex
▴ 350
172
votes
34
replies
26k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r
books
bioconductor
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Michael
54k
103
votes
34
replies
113k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 3 months ago by
Ram
43k • written 11.9 years ago by
GPR
▴ 390
121
votes
33
replies
39k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 12 months ago by
carlopecoraro2
★ 2.5k • written 10.7 years ago by
Eric Normandeau
11k
10
votes
33
replies
3.9k
views
Looking for a tool like fastq screen but for ONT data
gridion
nanopore
ont
minion
updated 10 months ago by
Ram
43k • written 5.8 years ago by
Rox
★ 1.4k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
11
votes
31
replies
14k
views
6 follow
How to concatenate multiple fasta file
sequence
genome
updated 11 months ago by
doggie
• 0 • written 5.7 years ago by
fec2
▴ 50
120
votes
31
replies
199k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Eric Normandeau
11k
147
votes
31
replies
138k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 9 months ago by
Ram
43k • written 12.2 years ago by
Anima Mundi
★ 2.9k
105
votes
31
replies
95k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 4 months ago by
mmfansler
▴ 450 • written 12.8 years ago by
2184687-1231-83-
★ 5.1k
50
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 5 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
47
votes
30
replies
4.3k
views
10 follow
Forum:
Bioinformatics software distribution
software
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 10 months ago by
Ram
43k • written 6.0 years ago by
Jennifer Pham
▴ 450
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Biostar User
★ 1.0k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Khader Shameer
18k
18
votes
30
replies
10k
views
6 follow
Tool:
Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina
BBMap
filterbytile
updated 10 months ago by
Ram
43k • written 7.4 years ago by
Brian Bushnell
20k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.2 years ago by
Obi Griffith
20k
20
votes
29
replies
2.5k
views
6 follow
Using bcftools to find unique alt homozygous sites
bcftools
updated 6 months ago by
Pierre Lindenbaum
161k • written 6 months ago by
Axzd
▴ 70
16
votes
29
replies
1.7k
views
Gene labels problem in enhanced volcano
R
ggplot2
enhancedvolcano
updated 12 weeks ago by
Mensur Dlakic
★ 27k • written 3 months ago by
anasjamshed
▴ 120
124
votes
29
replies
7.3k
views
18 follow
What License Do You Use When You Release Code And Data?
software
general
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Simon Cockell
7.4k
4
votes
29
replies
11k
views
6 follow
WGCNA soft thresholding problem
WGCNA
RNA-Seq
soft thresholding
data normalization
updated 9 weeks ago by
foejvs546
▴ 10 • written 5.4 years ago by
catagui
▴ 40
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 7 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
16k
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
3 months ago by
Jeremy Leipzig
22k
43
votes
28
replies
5.6k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Eric Normandeau
11k
28
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 8 hours ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
3
votes
27
replies
2.6k
views
7 follow
Forum:
What server do you use?
HPC
AWS
updated 11 months ago by
Ram
43k • written 5.8 years ago by
caggtaagtat
★ 1.9k
197
votes
27
replies
35k
views
20 follow
Forum:
Bioinformatics Cartoon
bioinformatics
updated 9 months ago by
Ram
43k • written 12.3 years ago by
Maxime Lamontagne
★ 2.3k
26
votes
27
replies
2.1k
views
10 follow
Forum:
Determining computer time required
computer
hpc
time
updated 3 months ago by
dsull
★ 5.9k • written 3 months ago by
Rozita
▴ 40
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 29 days ago by
sgv
• 0 • written 4.4 years ago by
Flo
▴ 240
27
votes
27
replies
10k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp
allele
biomart
dbsnp
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Michael
54k
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 10.2 years ago by
Istvan Albert
100k
28
votes
27
replies
15k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython
python
fastq
next-gen-sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Darked89
4.6k
103
votes
27
replies
89k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 11 months ago by
NIRJHAR
• 0 • written 11.9 years ago by
Rubal7
▴ 830
41
votes
27
replies
6.0k
views
8 follow
Forum:
Why bioinformaticians need to know programming languages?
Python
R
Programming
updated 11 months ago by
Ram
43k • written 6.9 years ago by
nilo
▴ 90
76
votes
26
replies
120k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 5 months ago by
cschu181
★ 2.8k • written 9.0 years ago by
Chenglin
▴ 260
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 7 months ago by
zx8754
11k • written 11.3 years ago by
henryvuong
▴ 810
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 7 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.6k
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 6 months ago by
Ram
43k • written 14.2 years ago by
User 59
13k
20
votes
26
replies
3.2k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment
fasta
image
updated 9 months ago by
Joe
21k • written 4.9 years ago by
Joel Wallenius
▴ 210
24
votes
26
replies
2.1k
views
6 follow
Forum:
Organizing a Bioinformatics Conference ?
meeting
conference
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Pierre Lindenbaum
161k
47
votes
26
replies
4.1k
views
11 follow
Blog:
Evolution of Biostars
meta
Biostars
updated 8 months ago by
aldhairmedico
▴ 70 • written 5.2 years ago by
venu
7.1k
38
votes
26
replies
19k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.2 years ago by
biostart
▴ 370
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner
snp
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
3
votes
26
replies
2.0k
views
6 follow
STAR Genome index Error
STAR
updated 7 months ago by
Ram
43k • written 7 months ago by
Prasanna
• 0
24
votes
26
replies
3.6k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 10 months ago by
Ram
43k • written 4.5 years ago by
German.M.Demidov
★ 2.9k
7
votes
25
replies
11k
views
6 follow
Tool:
MIGEC: towards error-free profiling of immune repertoires
sequencing-error
tcr
antibody
molecular-barcode
updated 10 months ago by
Ram
43k • written 10.0 years ago by
mikhail.shugay
3.5k
69
votes
25
replies
7.0k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Dave Gerrard
▴ 190
13,539 results • Page
2 of 271
Recent Votes
Convert sra to bam file error handling
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
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Comment: Post-imputation plot
by
LChart
3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
Comment: Does comparing two different groups to a common third group introduce bias in th
by
Qroid
▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
by
anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA
by
jared.andrews07
★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
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