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1,000 results • Page
2 of 20
Sort: replies
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Views
Votes
Replies
32
votes
51
replies
17k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq
samtools
bedtools
bam
updated 11.3 years ago by
brentp
24k • written 11.3 years ago by
User 9996
▴ 830
61
votes
51
replies
20k
views
9 follow
Tool:
Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
next-gen
sff
Tool
sequence
fastq
updated 16 months ago by
Ram
38k • written 8.9 years ago by
BioApps
▴ 790
179
votes
51
replies
15k
views
26 follow
I Am Preparing A Course On Ngs: Any Suggestion ?
next-gen
sequencing
galaxy
updated 9.7 years ago by
sarahhunter
▴ 600 • written 12.4 years ago by
Pierre Lindenbaum
153k
12
votes
50
replies
2.8k
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
6.1 years ago by
thomas.f.hahn2
▴ 100
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 7 weeks ago by
Ram
38k • written 7.9 years ago by
fhsantanna
▴ 610
93
votes
50
replies
14k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 28 days ago by
Ram
38k • written 9.3 years ago by
Istvan Albert
97k
26
votes
50
replies
11k
views
8 follow
Tool:
Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta
multi-fasta
retrieval
large file
illumina
Tool
updated 6.8 years ago by
shenwei356
8.0k • written 6.8 years ago by
hcwang
▴ 50
22
votes
50
replies
15k
views
Why I can not install anything on R?
R
software error
4.5 years ago by
Za
▴ 140
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 6 months ago by
Ram
38k • written 12.4 years ago by
Zhangleisdau
▴ 340
262
votes
48
replies
20k
views
37 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 4 weeks ago by
Lars
▴ 970 • written 7.9 years ago by
Deepak Tanwar
★ 4.2k
72
votes
48
replies
6.9k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 6 weeks ago by
Ram
38k • written 12.0 years ago by
User 59
13k
131
votes
48
replies
14k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 11.6 years ago by
Guangchuang Yu
★ 2.6k • written 11.6 years ago by
Eric Normandeau
11k
72
votes
48
replies
15k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 4 weeks ago by
Ram
38k • written 10.1 years ago by
lh3
33k
39
votes
48
replies
5.1k
views
CUTADAPT in windows
sequencing
updated 7 weeks ago by
Ram
38k • written 7.9 years ago by
fi1d18
★ 4.1k
68
votes
48
replies
6.9k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
errors
Forum
updated 5.5 years ago by
Charles Plessy
★ 2.9k • written 5.7 years ago by
Istvan Albert
97k
18
votes
47
replies
3.4k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
6.1 years ago by
dzisis1986
▴ 60
22
votes
47
replies
5.4k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 12.0 years ago by
Khader Shameer
18k • written 12.0 years ago by
Andrea_Bio
★ 2.8k
22
votes
47
replies
3.8k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 4.0 years ago by
gb
★ 2.2k • written 4.5 years ago by
fishgolden
▴ 460
43
votes
46
replies
3.1k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 6.5 years ago by
Ram
38k • written 6.5 years ago by
fi1d18
★ 4.1k
37
votes
46
replies
5.4k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 4.6 years ago by
Ram
38k • written 12.9 years ago by
Jeremy Leipzig
21k
92
votes
46
replies
10.0k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 6 weeks ago by
Ram
38k • written 11.7 years ago by
Andra Waagmeester
3.2k
105
votes
46
replies
11k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 29 days ago by
Ram
38k • written 9.6 years ago by
ugly.betty77
★ 1.1k
124
votes
46
replies
43k
views
20 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq
visualization
deeptools
ngsplot
homer
Forum
updated 20 months ago by
Chirag Nepal
★ 2.3k • written 7.1 years ago by
Sinji
★ 3.2k
106
votes
45
replies
80k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 6 months ago by
aswinssoman
▴ 20 • written 10.7 years ago by
Mchimich
▴ 320
184
votes
45
replies
29k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
general
pipeline
updated 18 months ago by
Ram
38k • written 13.1 years ago by
Giovanni M Dall'Olio
27k
20
votes
45
replies
10k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 9 weeks ago by
Ram
38k • written 7.9 years ago by
Ron
★ 1.1k
4
votes
45
replies
6.1k
views
SAM file wrong? help with validatesamfile
EXOME
Tutorial
updated 6.6 years ago by
Biostar
20 • written 6.8 years ago by
cristina_sabiers
▴ 110
235
votes
45
replies
69k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 11.8 years ago by
User 9126
▴ 50 • written 12.8 years ago by
Biomed
4.8k
152
votes
44
replies
28k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 9 months ago by
Ram
38k • written 9.2 years ago by
Carlos Borroto
★ 2.0k
99
votes
44
replies
21k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text
r
perl
python
updated 5.6 years ago by
grant.hovhannisyan
★ 2.5k • written 11.1 years ago by
John
★ 1.5k
24
votes
44
replies
12k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 7 months ago by
Ram
38k • written 7.4 years ago by
seta
★ 1.8k
126
votes
44
replies
27k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 20 days ago by
Ram
38k • written 6.5 years ago by
Lars
▴ 970
44
votes
44
replies
22k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 6 months ago by
Ram
38k • written 9.0 years ago by
Paul
★ 1.5k
102
votes
44
replies
7.7k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 4 weeks ago by
Ram
38k • written 9.6 years ago by
brentp
24k
21
votes
44
replies
2.8k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
2.6 years ago by
Kumar
▴ 150
194
votes
44
replies
68k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 11 weeks ago by
Ram
38k • written 10.5 years ago by
Obi Griffith
20k
121
votes
44
replies
19k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 6 weeks ago by
Ram
38k • written 12.8 years ago by
Madelaine Gogol
5.3k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 11 months ago by
Ram
38k • written 11.9 years ago by
Ryan D
★ 3.4k
16
votes
43
replies
5.4k
views
Stuck on calculating principal components
Vegan
R
software error
SNP
updated 5.3 years ago by
pfs
▴ 280 • written 5.3 years ago by
fi1d18
★ 4.1k
59
votes
43
replies
18k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 15 days ago by
Ram
38k • written 5.5 years ago by
Rox
★ 1.4k
31
votes
43
replies
17k
views
11 follow
Volcano plot help code
R
rna-seq
updated 4.8 years ago by
jordi.planells
▴ 450 • written 4.9 years ago by
anasofiamoreira94
▴ 80
66
votes
43
replies
25k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen
sequencing
parsing
fastq
programming
updated 14 months ago by
Ram
38k • written 12.2 years ago by
toni
★ 2.2k
57
votes
43
replies
14k
views
8 follow
Forum:
Best RNA-Seq aligner: A comparison of mapping tools
NGS
alignment
genome
RNA-Seq
sequence
updated 20 days ago by
Ram
38k • written 4.2 years ago by
David Langenberger
9.9k
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 6 months ago by
Ram
38k • written 13.0 years ago by
Yuri
★ 1.6k
19
votes
43
replies
4.0k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.6 years ago by
nazaninhoseinkhan
▴ 500
0
votes
42
replies
2.2k
views
Database from .gbk files
database
gbk
ncbi
2.8 years ago by
graysonford
• 0
8
votes
42
replies
3.6k
views
NaS (Nanopore Synthetic-long) help
Assembly
preprocessing
updated 12 weeks ago by
Ram
38k • written 7.8 years ago by
midox
▴ 290
122
votes
42
replies
8.7k
views
21 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 6 weeks ago by
Ram
38k • written 10.3 years ago by
Istvan Albert
97k
28
votes
42
replies
5.4k
views
7 follow
How to add tophat and bowtie to the path?
export PATH
bowtie2.2.9
tophat2
6.3 years ago by
mirza
▴ 180
11
votes
42
replies
2.9k
views
over presented kmer in fastq
fastqc
RNA-Seq
5.5 years ago by
Sam
▴ 150
1,000 results • Page
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Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
Answer: Somatic truth set
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Answer: Align miRNA library (small RNA-seq) without trimming
by
Ming Tommy Tang
★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression
by
afei
• 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa
by
rebeliscu
▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
by
cfos4698
▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking
by
Mensur Dlakic
★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error
by
Declan
• 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq
by
dsull
★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set
by
lethalfang
▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
Comment: GO enrichment analysis
by
Jeremy
▴ 780
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job?
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Carambakaracho
★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
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