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1,000 results • Page
2 of 20
Sort: replies
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Votes
Replies
61
votes
51
replies
22k
views
9 follow
Tool:
Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
sff
sequence
fastq
next-gen
updated 9 months ago by
Ram
43k • written 9.9 years ago by
BioApps
▴ 790
188
votes
50
replies
73k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 18 months ago by
Ram
43k • written 13.4 years ago by
Zhangleisdau
▴ 340
27
votes
50
replies
17k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 13 months ago by
Ram
43k • written 8.9 years ago by
fhsantanna
▴ 610
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 9 months ago by
Ram
43k • written 7.8 years ago by
hcwang
▴ 50
12
votes
50
replies
4.0k
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
7.1 years ago by
thomas.f.hahn2
▴ 100
91
votes
50
replies
52k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 2.4 years ago by
BioNovice247
▴ 20 • written 6.4 years ago by
rachel.kubik12
▴ 210
22
votes
50
replies
17k
views
Why I can not install anything on R?
R
software error
5.5 years ago by
Za
▴ 140
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 13 months ago by
Ram
43k • written 10.3 years ago by
Istvan Albert
100k
85
votes
49
replies
9.9k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective
general
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Jarretinha
3.4k
262
votes
48
replies
23k
views
37 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 13 months ago by
Lars
★ 1.0k • written 8.9 years ago by
Deepak Tanwar
★ 4.2k
39
votes
48
replies
6.8k
views
CUTADAPT in windows
sequencing
updated 13 months ago by
Ram
43k • written 8.9 years ago by
zizigolu
★ 4.3k
72
votes
48
replies
17k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 13 months ago by
Ram
43k • written 11.1 years ago by
lh3
33k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 4 months ago by
Ram
43k • written 10.4 years ago by
Irsan
★ 7.8k
72
votes
48
replies
8.3k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 13 months ago by
Ram
43k • written 13.0 years ago by
User 59
13k
68
votes
48
replies
8.6k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
updated 10 months ago by
Ram
43k • written 6.7 years ago by
Istvan Albert
100k
131
votes
48
replies
16k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 12.6 years ago by
Guangchuang Yu
★ 2.6k • written 12.6 years ago by
Eric Normandeau
11k
18
votes
47
replies
4.6k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
7.1 years ago by
dzisis1986
▴ 70
22
votes
47
replies
5.1k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 5.0 years ago by
gb
★ 2.2k • written 5.5 years ago by
fishgolden
▴ 510
23
votes
47
replies
7.0k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 13.0 years ago by
Khader Shameer
18k • written 13.0 years ago by
Andrea_Bio
★ 2.8k
188
votes
47
replies
2.7k
views
16 follow
Job:
Bioinformatics freelancers needed
freelancer
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Bioinfexperts
▴ 190
176
votes
46
replies
18k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
4 months ago by
Istvan Albert
100k
105
votes
46
replies
13k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 13 months ago by
Ram
43k • written 10.6 years ago by
ugly.betty77
★ 1.1k
37
votes
46
replies
6.7k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 5.6 years ago by
Ram
43k • written 13.9 years ago by
Jeremy Leipzig
22k
43
votes
46
replies
4.2k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 7.5 years ago by
Ram
43k • written 7.5 years ago by
zizigolu
★ 4.3k
82
votes
46
replies
8.3k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 15 days ago by
LauferVA
4.1k • written 9 months ago by
Sasha
▴ 830
125
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 11 months ago by
Ram
43k • written 8.1 years ago by
Sinji
★ 3.2k
92
votes
46
replies
12k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 13 months ago by
Ram
43k • written 12.7 years ago by
Andra Waagmeester
3.2k
4
votes
45
replies
7.6k
views
SAM file wrong? help with validatesamfile
EXOME
updated 11 months ago by
Ram
43k • written 7.8 years ago by
cristina_sabiers
▴ 110
108
votes
45
replies
86k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 19 months ago by
aswinssoman
▴ 70 • written 11.7 years ago by
Mchimich
▴ 320
185
votes
45
replies
31k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
22
votes
45
replies
13k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 14 months ago by
Ram
43k • written 8.9 years ago by
Ron
★ 1.2k
236
votes
45
replies
72k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 12.8 years ago by
User 9126
▴ 50 • written 13.8 years ago by
Biomed
4.9k
130
votes
44
replies
33k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 12 months ago by
Ram
43k • written 7.5 years ago by
Lars
★ 1.0k
122
votes
44
replies
11k
views
24 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 5 months ago by
Ram
43k • written 11.3 years ago by
Istvan Albert
100k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 9 days ago by
Michael
54k • written 14.0 years ago by
Yuri
★ 1.7k
43
votes
44
replies
5.4k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics
amplicon
macbook
Intel
MacOs
updated 5 months ago by
steve
★ 3.5k • written 5 months ago by
l.gallucci
▴ 10
46
votes
44
replies
24k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 18 months ago by
Ram
43k • written 10.0 years ago by
Paul
★ 1.5k
196
votes
44
replies
71k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 14 months ago by
Ram
43k • written 11.5 years ago by
Obi Griffith
20k
155
votes
44
replies
31k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 21 months ago by
Ram
43k • written 10.2 years ago by
Carlos Borroto
★ 2.1k
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 23 months ago by
Ram
43k • written 12.9 years ago by
Ryan D
★ 3.4k
121
votes
44
replies
21k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 13 months ago by
Ram
43k • written 13.8 years ago by
Madelaine Gogol
5.3k
21
votes
44
replies
4.2k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
3.6 years ago by
Kumar
▴ 170
27
votes
44
replies
14k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 19 months ago by
Ram
43k • written 8.4 years ago by
seta
★ 1.9k
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 6.6 years ago by
grant.hovhannisyan
★ 2.6k • written 12.1 years ago by
John
★ 1.5k
102
votes
44
replies
9.0k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 13 months ago by
Ram
43k • written 10.6 years ago by
brentp
24k
1
vote
43
replies
3.8k
views
Database from .gbk files
database
gbk
ncbi
updated 11 months ago by
Raul
• 0 • written 3.8 years ago by
graysonford
▴ 10
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 12 months ago by
Ram
43k • written 5.2 years ago by
David Langenberger
11k
19
votes
43
replies
5.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.6 years ago by
nazaninhoseinkhan
▴ 520
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 12 months ago by
Ram
43k • written 6.5 years ago by
Rox
★ 1.4k
66
votes
43
replies
27k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen
sequencing
parsing
fastq
programming
updated 2.2 years ago by
Ram
43k • written 13.2 years ago by
toni
★ 2.2k
1,000 results • Page
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Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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