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117,057 results • Page
2 of 2342
Sort: replies
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Votes
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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 10 months ago by
Ram
44k • written 10.1 years ago by
BioApps
▴ 790
188
votes
50
replies
74k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 20 months ago by
Ram
44k • written 13.6 years ago by
Zhangleisdau
▴ 340
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
44k • written 10.5 years ago by
Istvan Albert
100k
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
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
44k • written 8.0 years ago by
hcwang
▴ 50
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
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
44k • written 9.0 years ago by
fhsantanna
▴ 620
85
votes
49
replies
10k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective
general
updated 6 months ago by
Ram
44k • written 14.2 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
8.6k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 15 months ago by
Ram
44k • written 13.1 years ago by
User 59
13k
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
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
44k • written 6.9 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
44k • written 10.6 years ago by
Irsan
★ 7.8k
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 15 months ago by
Ram
44k • written 11.3 years ago by
lh3
33k
39
votes
48
replies
7.1k
views
CUTADAPT in windows
sequencing
updated 15 months ago by
Ram
44k • written 9.0 years ago by
zizigolu
★ 4.3k
22
votes
47
replies
5.4k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 5.2 years ago by
gb
★ 2.2k • written 5.6 years ago by
fishgolden
▴ 510
18
votes
47
replies
4.8k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
7.3 years ago by
dzisis1986
▴ 70
188
votes
47
replies
3.0k
views
16 follow
Job:
Bioinformatics freelancers needed
freelancer
updated 13 months ago by
Ram
44k • written 8.1 years ago by
Bioinfexperts
▴ 190
23
votes
47
replies
7.2k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 13.2 years ago by
Khader Shameer
18k • written 13.2 years ago by
Andrea_Bio
★ 2.8k
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
44k • written 8.2 years ago by
Sinji
★ 3.2k
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
44k • written 7.6 years ago by
zizigolu
★ 4.3k
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
44k • written 10.7 years ago by
ugly.betty77
★ 1.1k
85
votes
46
replies
9.3k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 9 weeks ago by
LauferVA
4.2k • written 11 months ago by
Sasha
▴ 850
37
votes
46
replies
7.1k
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
44k • 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
44k • 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
6 months ago by
Istvan Albert
100k
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
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 7 months ago by
Ram
44k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
4
votes
45
replies
7.9k
views
SAM file wrong? help with validatesamfile
EXOME
updated 13 months ago by
Ram
44k • 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 16 months ago by
Ram
44k • written 9.0 years ago by
Ron
★ 1.2k
108
votes
45
replies
87k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 20 months ago by
aswinssoman
▴ 80 • written 11.8 years ago by
Mchimich
▴ 320
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
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
44k • written 11.5 years ago by
Istvan Albert
100k
197
votes
44
replies
72k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 16 months ago by
Ram
44k • written 11.7 years ago by
Obi Griffith
20k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 8 weeks ago by
Michael
54k • written 14.2 years ago by
Yuri
★ 1.7k
155
votes
44
replies
32k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 23 months ago by
Ram
44k • written 10.3 years ago by
Carlos Borroto
★ 2.1k
102
votes
44
replies
9.1k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 14 months ago by
Ram
44k • written 10.8 years ago by
brentp
24k
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
44k • written 7.7 years ago by
Lars
★ 1.0k
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
44k • written 8.5 years ago by
seta
★ 1.9k
43
votes
44
replies
6.2k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics
amplicon
macbook
Intel
MacOs
updated 7 months ago by
steve
★ 3.5k • written 7 months ago by
l.gallucci
▴ 10
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
44k • written 13.9 years ago by
Madelaine Gogol
5.3k
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 2.1 years ago by
Ram
44k • written 13.1 years ago by
Ryan D
★ 3.4k
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
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
44k • written 10.1 years ago by
Paul
★ 1.5k
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
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
44k • written 5.3 years ago by
David Langenberger
11k
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
19
votes
43
replies
5.7k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.8 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 14 months ago by
Ram
44k • written 6.7 years ago by
Rox
★ 1.4k
117,057 results • Page
2 of 2342
Recent Votes
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
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Comment: Super ehancers
by
jared.andrews07
★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
finch
• 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
Answer: Is it possible to run CibersortX with a very small number of samples?
by
finch
• 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Ram
44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
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