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116,925 results • Page
2 of 2339
Sort: replies
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Votes
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32
votes
51
replies
20k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq
samtools
bedtools
bam
updated 12.4 years ago by
brentp
24k • written 12.4 years ago by
User 9996
▴ 840
188
votes
50
replies
73k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 19 months ago by
Ram
43k • written 13.6 years ago by
Zhangleisdau
▴ 340
27
votes
50
replies
18k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 15 months ago by
Ram
43k • written 9.0 years ago by
fhsantanna
▴ 620
94
votes
50
replies
53k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 2.5 years ago by
BioNovice247
▴ 20 • written 6.5 years ago by
rachel.kubik12
▴ 220
12
votes
50
replies
4.2k
views
How can I find out the Linux version and what is the ftp command to install R and R Studio on Linux server?
R
7.2 years ago by
thomas.f.hahn2
▴ 100
93
votes
50
replies
16k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Istvan Albert
100k
22
votes
50
replies
17k
views
Why I can not install anything on R?
R
software error
5.6 years ago by
Za
▴ 140
26
votes
50
replies
14k
views
8 follow
Tool:
Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta
multi-fasta
illumina
updated 10 months ago by
Ram
43k • written 8.0 years ago by
hcwang
▴ 50
85
votes
49
replies
10k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective
general
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Jarretinha
3.4k
262
votes
48
replies
23k
views
37 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 14 months ago by
Lars
★ 1.0k • written 9.0 years ago by
Deepak Tanwar
★ 4.2k
72
votes
48
replies
8.5k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 15 months ago by
Ram
43k • written 13.1 years ago by
User 59
13k
72
votes
48
replies
18k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 14 months ago by
Ram
43k • written 11.3 years ago by
lh3
33k
68
votes
48
replies
8.9k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
updated 12 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
90
votes
48
replies
34k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
39
votes
48
replies
7.0k
views
CUTADAPT in windows
sequencing
updated 15 months ago by
Ram
43k • written 9.0 years ago by
zizigolu
★ 4.3k
131
votes
48
replies
16k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 12.8 years ago by
Guangchuang Yu
★ 2.6k • written 12.8 years ago by
Eric Normandeau
11k
188
votes
47
replies
2.9k
views
16 follow
Job:
Bioinformatics freelancers needed
freelancer
updated 13 months ago by
Ram
43k • written 8.1 years ago by
Bioinfexperts
▴ 190
22
votes
47
replies
5.3k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 5.1 years ago by
gb
★ 2.2k • written 5.6 years ago by
fishgolden
▴ 510
18
votes
47
replies
4.7k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
7.3 years ago by
dzisis1986
▴ 70
23
votes
47
replies
7.2k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 13.1 years ago by
Khader Shameer
18k • written 13.1 years ago by
Andrea_Bio
★ 2.8k
105
votes
46
replies
13k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 14 months ago by
Ram
43k • written 10.7 years ago by
ugly.betty77
★ 1.1k
83
votes
46
replies
9.1k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 8 weeks ago by
LauferVA
4.2k • written 11 months ago by
Sasha
▴ 840
126
votes
46
replies
50k
views
21 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization
ChIP-Seq
homer
ngsplot
deeptools
updated 13 months ago by
Ram
43k • written 8.2 years ago by
Sinji
★ 3.2k
37
votes
46
replies
7.0k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 5.7 years ago by
Ram
43k • written 14.1 years ago by
Jeremy Leipzig
22k
92
votes
46
replies
12k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 15 months ago by
Ram
43k • written 12.9 years ago by
Andra Waagmeester
3.2k
176
votes
46
replies
19k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
5 months ago by
Istvan Albert
100k
43
votes
46
replies
4.3k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 7.6 years ago by
Ram
43k • written 7.6 years ago by
zizigolu
★ 4.3k
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
108
votes
45
replies
86k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 20 months ago by
aswinssoman
▴ 70 • written 11.8 years ago by
Mchimich
▴ 320
237
votes
45
replies
72k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 12.9 years ago by
User 9126
▴ 50 • written 14.0 years ago by
Biomed
5.0k
4
votes
45
replies
7.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 13 months ago by
Ram
43k • written 7.9 years ago by
cristina_sabiers
▴ 110
22
votes
45
replies
13k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Ron
★ 1.2k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 7 weeks ago by
Michael
54k • written 14.2 years ago by
Yuri
★ 1.7k
121
votes
44
replies
21k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 15 months ago by
Ram
43k • written 13.9 years ago by
Madelaine Gogol
5.3k
99
votes
44
replies
24k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text
r
perl
python
updated 6.7 years ago by
grant.hovhannisyan
★ 2.6k • written 12.2 years ago by
John
★ 1.5k
122
votes
44
replies
11k
views
24 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 6 months ago by
Ram
43k • written 11.5 years ago by
Istvan Albert
100k
196
votes
44
replies
72k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 16 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
102
votes
44
replies
9.1k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 14 months ago by
Ram
43k • written 10.7 years ago by
brentp
24k
155
votes
44
replies
32k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 22 months ago by
Ram
43k • written 10.3 years ago by
Carlos Borroto
★ 2.1k
27
votes
44
replies
15k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 21 months ago by
Ram
43k • written 8.5 years ago by
seta
★ 1.9k
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 2.1 years ago by
Ram
43k • written 13.1 years ago by
Ryan D
★ 3.4k
46
votes
44
replies
25k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 20 months ago by
Ram
43k • written 10.1 years ago by
Paul
★ 1.5k
43
votes
44
replies
6.0k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics
amplicon
macbook
Intel
MacOs
updated 6 months ago by
steve
★ 3.5k • written 7 months ago by
l.gallucci
▴ 10
21
votes
44
replies
4.4k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
3.8 years ago by
Kumar
▴ 170
130
votes
44
replies
34k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 14 months ago by
Ram
43k • written 7.7 years ago by
Lars
★ 1.0k
19
votes
43
replies
5.6k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by
nazaninhoseinkhan
▴ 520
31
votes
43
replies
20k
views
11 follow
Volcano plot help code
R
rna-seq
updated 5.9 years ago by
jordi.planells
▴ 480 • written 6.1 years ago by
anasofiamoreira94
▴ 80
16
votes
43
replies
6.8k
views
Stuck on calculating principal components
Vegan
R
software error
SNP
updated 6.5 years ago by
pfs
▴ 280 • written 6.5 years ago by
zizigolu
★ 4.3k
57
votes
43
replies
16k
views
8 follow
Forum:
Best RNA-Seq aligner: A comparison of mapping tools
NGS
alignment
genome
RNA-Seq
sequence
updated 14 months ago by
Ram
43k • written 5.3 years ago by
David Langenberger
11k
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 14 months ago by
Ram
43k • written 6.7 years ago by
Rox
★ 1.4k
116,925 results • Page
2 of 2339
Recent Votes
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
Split multiallelic SNPs to biallelic from vcf
Filtering multi-allelic sites in VCF files
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Recent Replies
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
• 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content
by
ntsopoul
▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content
by
ATpoint
82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object
by
ATpoint
82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴ 40
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
by
GenoMax
142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq
by
ATpoint
82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
Comment: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
Which species is this?
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
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