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110,515 results • Page
2 of 2211
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 11.5 years ago by
brentp
24k • written 11.5 years ago by
User 9996
▴ 840
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 18 months ago by
Ram
39k • written 9.1 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 9.9 years ago by
sarahhunter
▴ 600 • written 12.6 years ago by
Pierre Lindenbaum
154k
12
votes
50
replies
2.9k
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
6.2 years ago by
thomas.f.hahn2
▴ 100
22
votes
50
replies
15k
views
Why I can not install anything on R?
R
software error
4.6 years ago by
Za
▴ 140
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 7.0 years ago by
shenwei356
8.1k • written 7.0 years ago by
hcwang
▴ 50
188
votes
50
replies
68k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 8 months ago by
Ram
39k • written 12.6 years ago by
Zhangleisdau
▴ 340
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 3 months ago by
Ram
39k • written 8.1 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 3 months ago by
Ram
39k • written 9.5 years ago by
Istvan Albert
98k
262
votes
48
replies
21k
views
37 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 3 months ago by
Lars
▴ 970 • written 8.1 years ago by
Deepak Tanwar
★ 4.2k
39
votes
48
replies
5.2k
views
CUTADAPT in windows
sequencing
updated 3 months ago by
Ram
39k • written 8.1 years ago by
fi1d18
★ 4.2k
72
votes
48
replies
16k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 3 months ago by
Ram
39k • written 10.3 years ago by
lh3
33k
131
votes
48
replies
14k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 11.8 years ago by
Guangchuang Yu
★ 2.6k • written 11.8 years ago by
Eric Normandeau
11k
72
votes
48
replies
7.1k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 3 months ago by
Ram
39k • written 12.1 years ago by
User 59
13k
68
votes
48
replies
7.1k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
updated 25 days ago by
Ram
39k • written 5.9 years ago by
Istvan Albert
98k
22
votes
47
replies
4.0k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 4.2 years ago by
gb
★ 2.2k • written 4.7 years ago by
fishgolden
▴ 460
188
votes
47
replies
1.3k
views
16 follow
Job:
Bioinformatics freelancers needed
freelancer
updated 8 weeks ago by
Ram
39k • written 7.1 years ago by
Bioinfexperts
▴ 190
18
votes
47
replies
3.6k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
6.3 years ago by
dzisis1986
▴ 60
22
votes
47
replies
5.6k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 12.2 years ago by
Khader Shameer
18k • written 12.2 years ago by
Andrea_Bio
★ 2.8k
43
votes
46
replies
3.2k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 6.7 years ago by
Ram
39k • written 6.7 years ago by
fi1d18
★ 4.2k
92
votes
46
replies
10k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 3 months ago by
Ram
39k • written 11.9 years ago by
Andra Waagmeester
3.2k
37
votes
46
replies
5.6k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 4.7 years ago by
Ram
39k • written 13.1 years ago by
Jeremy Leipzig
21k
105
votes
46
replies
12k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 3 months ago by
Ram
39k • written 9.8 years ago by
ugly.betty77
★ 1.1k
125
votes
46
replies
44k
views
20 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization
ChIP-Seq
homer
ngsplot
deeptools
updated 8 weeks ago by
Ram
39k • written 7.3 years ago by
Sinji
★ 3.2k
20
votes
45
replies
11k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 4 months ago by
Ram
39k • written 8.1 years ago by
Ron
★ 1.1k
106
votes
45
replies
81k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 9 months ago by
aswinssoman
▴ 30 • written 10.9 years ago by
Mchimich
▴ 320
184
votes
45
replies
30k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
general
pipeline
updated 20 months ago by
Ram
39k • written 13.3 years ago by
Giovanni M Dall'Olio
27k
4
votes
45
replies
6.3k
views
SAM file wrong? help with validatesamfile
EXOME
updated 8 weeks ago by
Ram
39k • written 7.0 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 12.0 years ago by
User 9126
▴ 50 • written 13.0 years ago by
Biomed
4.9k
102
votes
44
replies
7.9k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 3 months ago by
Ram
39k • written 9.8 years ago by
brentp
24k
21
votes
44
replies
3.0k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
2.8 years ago by
Kumar
▴ 170
90
votes
44
replies
58k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 13 months ago by
Ram
39k • written 12.1 years ago by
Ryan D
★ 3.4k
25
votes
44
replies
12k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 9 months ago by
Ram
39k • written 7.6 years ago by
seta
★ 1.8k
126
votes
44
replies
28k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 12 weeks ago by
Ram
39k • written 6.7 years ago by
Lars
▴ 970
99
votes
44
replies
22k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text
r
perl
python
updated 5.8 years ago by
grant.hovhannisyan
★ 2.5k • written 11.2 years ago by
John
★ 1.5k
121
votes
44
replies
19k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 3 months ago by
Ram
39k • written 13.0 years ago by
Madelaine Gogol
5.3k
44
votes
44
replies
23k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 8 months ago by
Ram
39k • written 9.1 years ago by
Paul
★ 1.5k
152
votes
44
replies
29k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 11 months ago by
Ram
39k • written 9.4 years ago by
Carlos Borroto
★ 2.0k
196
votes
44
replies
69k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 4 months ago by
Ram
39k • written 10.7 years ago by
Obi Griffith
20k
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 16 months ago by
Ram
39k • written 12.4 years ago by
toni
★ 2.2k
19
votes
43
replies
4.2k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.8 years ago by
nazaninhoseinkhan
▴ 510
185
votes
43
replies
79k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 9 months ago by
Ram
39k • written 13.2 years ago by
Yuri
★ 1.6k
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 12 weeks ago by
Ram
39k • written 4.4 years ago by
David Langenberger
9.9k
170
votes
43
replies
16k
views
25 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
updated 5 weeks ago by
zx8754
11k • written 10.2 years ago by
Istvan Albert
98k
31
votes
43
replies
17k
views
11 follow
Volcano plot help code
R
rna-seq
updated 5.0 years ago by
jordi.planells
▴ 450 • written 5.1 years ago by
anasofiamoreira94
▴ 80
16
votes
43
replies
5.6k
views
Stuck on calculating principal components
Vegan
R
software error
SNP
updated 5.5 years ago by
pfs
▴ 280 • written 5.5 years ago by
fi1d18
★ 4.2k
1
vote
43
replies
2.5k
views
Database from .gbk files
database
gbk
ncbi
updated 7 weeks ago by
Raul
• 0 • written 3.0 years ago by
graysonford
▴ 10
59
votes
43
replies
19k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 12 weeks ago by
Ram
39k • written 5.7 years ago by
Rox
★ 1.4k
138
votes
42
replies
20k
views
22 follow
Forum:
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 10 weeks ago by
Vincent Laufer
★ 2.9k • written 10.0 years ago by
Whetting
★ 1.6k
28
votes
42
replies
5.6k
views
7 follow
How to add tophat and bowtie to the path?
export PATH
bowtie2.2.9
tophat2
6.5 years ago by
mirza
▴ 180
110,515 results • Page
2 of 2211
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
Zhichao
• 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2
by
ATpoint
72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts
by
ATpoint
72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
ATpoint
72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
Thanks a lot, it works
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Answer: Extract sequences from a fastq file by a list of IDs
by
GenoMax
129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
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