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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 11.2 years ago by
brentp
24k • written 11.2 years ago by
User 9996
▴ 820
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 14 months ago by
Ram
37k • written 8.8 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 9.5 years ago by
sarahhunter
▴ 600 • written 12.3 years ago by
Pierre Lindenbaum
152k
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
16s
fasta
extract
updated 1 day ago by
Ram
37k • written 7.8 years ago by
fhsantanna
▴ 600
12
votes
50
replies
2.7k
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
5.9 years ago by
thomas.f.hahn2
▴ 100
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 4 months ago by
Ram
37k • written 12.3 years ago by
Zhangleisdau
▴ 340
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 6.6 years ago by
shenwei356
7.8k • written 6.7 years ago by
hcwang
▴ 50
93
votes
50
replies
14k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
Forum
updated 9.2 years ago by
amcrisan
▴ 370 • written 9.2 years ago by
Istvan Albert
96k
22
votes
50
replies
15k
views
Why I can not install anything on R?
R
software error
4.3 years ago by
Za
▴ 140
72
votes
48
replies
6.7k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
tutorial
education
updated 11.8 years ago by
Gareth Palidwor
★ 1.6k • written 11.8 years ago by
User 59
13k
39
votes
48
replies
5.0k
views
CUTADAPT in windows
sequencing
updated 10 days ago by
Ram
37k • written 7.8 years ago by
fi1d18
★ 4.1k
72
votes
48
replies
15k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa
alignment
ngs
tutorial
Tutorial
updated 10 months ago by
Ram
37k • written 10.0 years ago by
lh3
33k
131
votes
48
replies
14k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 11.5 years ago by
Guangchuang Yu
★ 2.6k • written 11.5 years ago by
Eric Normandeau
11k
68
votes
48
replies
6.8k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
errors
Forum
updated 5.3 years ago by
Charles Plessy
★ 2.9k • written 5.6 years ago by
Istvan Albert
96k
261
votes
47
replies
20k
views
35 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 4 weeks ago by
Ram
37k • written 7.7 years ago by
Deepak Tanwar
★ 4.2k
18
votes
47
replies
3.3k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
6.0 years ago by
dzisis1986
▴ 60
22
votes
47
replies
3.7k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 3.9 years ago by
gb
★ 2.1k • written 4.3 years ago by
fishgolden
▴ 460
22
votes
47
replies
5.4k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 11.9 years ago by
Khader Shameer
18k • written 11.9 years ago by
Andrea_Bio
★ 2.8k
124
votes
46
replies
42k
views
20 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq
visualization
deeptools
ngsplot
homer
Forum
updated 18 months ago by
Chirag Nepal
★ 2.3k • written 6.9 years ago by
Sinji
★ 3.2k
37
votes
46
replies
5.3k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 4.4 years ago by
Ram
37k • written 12.8 years ago by
Jeremy Leipzig
21k
92
votes
46
replies
9.8k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
bioinformatics
programming
subjective
updated 6.7 years ago by
Biostar
20 • written 11.6 years ago by
Andra Waagmeester
3.2k
43
votes
46
replies
3.1k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 6.3 years ago by
Ram
37k • written 6.3 years ago by
fi1d18
★ 4.1k
105
votes
46
replies
11k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Forum
written 9.4 years ago by
ugly.betty77
★ 1.1k
106
votes
45
replies
79k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 5 months ago by
aswinssoman
▴ 20 • written 10.5 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 16 months ago by
Ram
37k • written 12.9 years ago by
Giovanni M Dall'Olio
27k
4
votes
45
replies
5.9k
views
SAM file wrong? help with validatesamfile
EXOME
Tutorial
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
cristina_sabiers
▴ 110
20
votes
45
replies
10k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 12 days ago by
Ram
37k • written 7.7 years ago by
Ron
★ 1.1k
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 11.6 years ago by
User 9126
▴ 50 • written 12.7 years ago by
Biomed
4.8k
44
votes
44
replies
22k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 4 months ago by
Ram
37k • written 8.8 years ago by
Paul
★ 1.5k
152
votes
44
replies
28k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 7 months ago by
Ram
37k • written 9.0 years ago by
Carlos Borroto
★ 2.0k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 9 months ago by
Ram
37k • written 11.8 years ago by
Ryan D
★ 3.4k
102
votes
44
replies
7.7k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
bioinformatics
updated 2.1 years ago by
ATpoint
68k • written 9.5 years ago by
brentp
24k
121
votes
44
replies
18k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
job
subjective
updated 6.6 years ago by
5heikki
11k • written 12.6 years ago by
Madelaine Gogol
5.3k
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 5.4 years ago by
grant.hovhannisyan
★ 2.5k • written 10.9 years ago by
John
★ 1.5k
126
votes
44
replies
27k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
RNA-Seq
NGS
adapter
Forum
written 6.4 years ago by
Lars
▴ 910
194
votes
44
replies
67k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 26 days ago by
Ram
37k • written 10.4 years ago by
Obi Griffith
20k
22
votes
44
replies
11k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 5 months ago by
Ram
37k • written 7.2 years ago by
seta
★ 1.7k
21
votes
44
replies
2.7k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
2.5 years ago by
Kumar
▴ 150
19
votes
43
replies
3.9k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.5 years ago by
nazaninhoseinkhan
▴ 490
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 12 months ago by
Ram
37k • written 12.0 years ago by
toni
★ 2.2k
16
votes
43
replies
5.2k
views
Stuck on calculating principal components
Vegan
R
software error
SNP
updated 5.2 years ago by
pfs
▴ 280 • written 5.2 years ago by
fi1d18
★ 4.1k
31
votes
43
replies
17k
views
11 follow
Volcano plot help code
R
rna-seq
updated 4.6 years ago by
jordi.planells
▴ 450 • written 4.8 years ago by
anasofiamoreira94
▴ 80
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 5 months ago by
Ram
37k • written 12.9 years ago by
Yuri
★ 1.6k
57
votes
43
replies
13k
views
8 follow
Forum:
Best RNA-Seq aligner: A comparison of mapping tools
RNA-Seq
NGS
alignment
genome
sequence
Forum
updated 24 months ago by
amy__
▴ 50 • written 4.0 years ago by
David Langenberger
9.8k
0
votes
42
replies
2.1k
views
Database from .gbk files
database
gbk
ncbi
2.6 years ago by
graysonford
• 0
122
votes
42
replies
8.6k
views
21 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
biostar
meta
News
updated 6.1 years ago by
jonasmst
▴ 400 • written 10.2 years ago by
Istvan Albert
96k
28
votes
42
replies
5.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH
bowtie2.2.9
tophat2
6.2 years ago by
mirza
▴ 180
57
votes
42
replies
5.0k
views
12 follow
Forum:
Why is academic software hard to install?
software-installation
updated 12 months ago by
Ram
37k • written 8.3 years ago by
lh3
33k
11
votes
42
replies
2.8k
views
over presented kmer in fastq
fastqc
RNA-Seq
5.3 years ago by
Sam
▴ 150
151
votes
42
replies
173k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 8 months ago by
Ram
37k • written 10.9 years ago by
Obi Griffith
20k
1,000 results • Page
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Deseq2 with one factor and multiple levels
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1000 genomes project reference panel - GRCh38
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Recent Replies
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
If you aren't willing to provide more precise information than this, sufficient for a reader to reproduce what you're seeing, I will delete…
Answer: Error while trying to install salmon
by
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▴ 10
Donwloading the package from conda (https://anaconda.org/conda-forge/boost/files?version=1.60.0) worked for me wget https://anaconda.org/…
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First issue is that GEO series matrix files can't be read using `read.delim`. Second issue is the data are from Agilent microarrays and …
Comment: PLINK2 selecting variants based on INFO score
by
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• 0
I have tried that (the .pvar file contains the "1:10586" form as ID which I mentioned above) which leads to the same output as above, 0 var…
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You can run any system command from inside R using `system()`. This works well if there is a single command without many dependencies. For …
Comment: samtools markdup in Rsamtools
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> But other solutions are also fine: bash, nextflow, snakemake
Answer: samtools markdup in Rsamtools
by
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68k
My honest opinion: Do processing of sequencing data on the standard command line with samtools. There is no need for the added complexity t…
Comment: To batch correct or analyse separately?
by
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★ 1.8k
Another great and up-to-date resource is this: https://www.sc-best-practices.org/preamble.html
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
The --exclude file must use the same variant IDs as your .pvar file. You should elaborate on what seemed to go wrong when you tried to arr…
Comment: phylogeny
by
炫
• 0
Hello, my problem is the same as yours, did you finally solve this problem?
Comment: phylogeny
by
炫
• 0
您好,我的问题和您的一模一样,请问您这个问题最终解决了吗
Comment: Issue with hmmcalibrate during tutorial.
by
apcreyes29
• 0
If that's the case then I'll just proceed then. Thank you!
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68k
Instead of writing that all down I recommend to read the relevant part of the Bioconductor scRNA-seq book (OSCA) which covers the "how's" a…
Answer: Issue with hmmcalibrate during tutorial.
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Pretty sure that `hmmcalibrate` does not exist in HMMer version 3+ as the models are internally calibrated. I think you are using a manual …
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▴ 10
Thank you for your reply. Your answer has helped me. I am a novice in scientific research, and the reading of literature is really poor. …
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