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410 results • Page
5 of 9
Sort: Votes
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Votes
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7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 10 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
7
votes
0
replies
5.3k
views
Tutorial:
Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 14 months ago by
Ram
43k • written 11.9 years ago by
Shuixia100
▴ 120
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 5 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
6
votes
0
replies
3.2k
views
Tutorial:
Uc Riverside Bioinformatics Manuals
computing-manuals
updated 14 months ago by
Ram
43k • written 12.0 years ago by
Sean Davis
26k
6
votes
1
reply
428
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
6
votes
2
replies
2.7k
views
Tutorial:
Tutorial Bioinformatics Static Website
website
updated 13 months ago by
Ram
43k • written 10.2 years ago by
rob234king
▴ 610
6
votes
10
replies
5.2k
views
Tutorial:
Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR
dna-methylation
updated 13 months ago by
Ram
43k • written 6.2 years ago by
dec986
▴ 370
6
votes
11
replies
5.7k
views
6 follow
Tutorial:
Add count numbers to headers in a fasta file
genome
updated 14 months ago by
Ram
43k • written 7.4 years ago by
wu.zhiqiang.1020
▴ 50
6
votes
0
replies
2.3k
views
Tutorial:
data.frames in R: How vectorization can save you time and heartache
R
3.1 years ago by
rpolicastro
13k
6
votes
1
reply
3.0k
views
Tutorial:
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq
peak-calling
sequencing
updated 13 months ago by
Ram
43k • written 10.0 years ago by
dnaseiseq
▴ 220
6
votes
0
replies
6.4k
views
Tutorial:
Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 14 months ago by
Ram
43k • written 12.0 years ago by
Biostar User
▴ 360
6
votes
3
replies
4.5k
views
Tutorial:
Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment
sequencing
RNA-seq
gene
updated 13 months ago by
Ram
43k • written 5.5 years ago by
contact
▴ 40
6
votes
0
replies
3.6k
views
Tutorial:
How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 13 months ago by
Ram
43k • written 9.9 years ago by
Philipp Bayer
8.3k
6
votes
0
replies
525
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 11 weeks ago by
zx8754
11k • written 11 weeks ago by
Ming Tommy Tang
★ 3.9k
6
votes
0
replies
1.6k
views
Tutorial:
NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar
structural-variation
updated 13 months ago by
Ram
43k • written 5.4 years ago by
lonphan
▴ 70
6
votes
2
replies
5.0k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
4 months ago by
GenoMax
141k
6
votes
3
replies
5.7k
views
Tutorial:
High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 14 months ago by
Ram
43k • written 11.8 years ago by
Istvan Albert
100k
6
votes
2
replies
4.2k
views
Tutorial:
GATK method for filtering vcf lines using GT values at all or multisample level.
genome
vcf
genotype
variant-filtration
updated 11 months ago by
Ram
43k • written 6.9 years ago by
kirannbishwa01
★ 1.6k
6
votes
4
replies
7.5k
views
Tutorial:
Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization
ChIP-seq
RNA-seq
ucsc-genome-browser
bigwig
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Sukhi Singh
11k
6
votes
0
replies
5.3k
views
Tutorial:
How to download GEO data Quickly and easily
geo
RNA-Seq
R
data-mining
14 months ago by
Novogene
▴ 420
6
votes
2
replies
1.6k
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
2.7 years ago by
Kevin Blighe
87k
6
votes
1
reply
2.5k
views
Tutorial:
Nice simple interactive Vim tutorial
vim
linux
updated 13 months ago by
Ram
43k • written 9.5 years ago by
Medhat
9.7k
6
votes
1
reply
7.8k
views
Tutorial:
Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat
RNA-seq
cufflinks
updated 14 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
5
votes
2
replies
2.3k
views
Tutorial:
Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA
closestBed
bedtools-closest
bedtools
updated 13 months ago by
Ram
43k • written 5.2 years ago by
linuxborg2
▴ 10
5
votes
2
replies
1.7k
views
Tutorial:
ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq
next-gen
ENCODE
updated 12 months ago by
Ram
43k • written 7.9 years ago by
Ar
★ 1.1k
5
votes
5
replies
6.9k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 130
5
votes
0
replies
2.2k
views
Tutorial:
Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm
meme
parallel
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Alex Reynolds
35k
5
votes
0
replies
1.1k
views
Tutorial:
Finding individual motif occurrences with FIMO from the MEME suite
motif
meme
jaspar
fimo
updated 13 months ago by
Ram
43k • written 5.4 years ago by
ATpoint
82k
5
votes
0
replies
1.7k
views
Tutorial:
Software Carpentry
programming
updated 14 months ago by
Ram
43k • written 12.0 years ago by
Philipp Bayer
8.3k
5
votes
0
replies
3.3k
views
Tutorial:
How to run CWL with Nextflow
cwl
nextflow
updated 13 months ago by
Ram
43k • written 4.2 years ago by
steve
★ 3.5k
5
votes
2
replies
3.1k
views
Tutorial:
Get GC Content from UCSC with perl script (mysql)
myql
ucsc
gc-content
perl
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Shicheng Guo
★ 9.4k
5
votes
0
replies
1.9k
views
Tutorial:
Gatk December Workshop Presentations
gatk
updated 14 months ago by
Ram
43k • written 11.3 years ago by
William
★ 5.3k
5
votes
1
reply
4.2k
views
Tutorial:
Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 16 months ago by
Ram
43k • written 8.8 years ago by
Philipp Bayer
8.3k
5
votes
0
replies
1.6k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
5
votes
3
replies
4.2k
views
Tutorial:
Chip Seq Review Papers
chip-seq
updated 14 months ago by
Ram
43k • written 11.4 years ago by
prtimilsina
▴ 80
5
votes
2
replies
2.3k
views
Tutorial:
NCBI submissions: SRA and TSA
NCBI
TSA
SRA
RNA-Seq
updated 13 months ago by
Ram
43k • written 5.4 years ago by
saraoppenheim
▴ 50
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 3 days ago by
ATpoint
82k • written 4 days ago by
BioinfGuru
★ 1.7k
5
votes
3
replies
5.4k
views
Tutorial:
bam2rpkm by bedtools
bam
RNA-Seq
bedtools
rpkm
updated 13 months ago by
toxin08x
• 0 • written 6.5 years ago by
jmzeng1314
▴ 130
4
votes
2
replies
2.8k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 7 months ago by
GenoMax
141k • written 4.0 years ago by
ATpoint
82k
4
votes
2
replies
1.1k
views
Tutorial:
How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC
transcription
factor
ChIP-seq
9 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
1
reply
1.4k
views
Tutorial:
Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED
BEDtools
updated 13 months ago by
Ram
43k • written 3.7 years ago by
sdsubaru33
▴ 40
4
votes
2
replies
7.2k
views
Tutorial:
Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink
gwas
updated 14 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
4
votes
0
replies
949
views
Tutorial:
How to make a heatmap in R and deep understand it
heatmap
r
11 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
0
replies
1.2k
views
Tutorial:
Long Read Genome Assembly Video Series
long-read
genome-assembly
2.9 years ago by
pbpanigrahi
▴ 420
4
votes
0
replies
1.8k
views
Tutorial:
NIH CDE browser for TCGA clinical data CDE codes
nih
tcga
metadata
cde
updated 13 months ago by
Ram
43k • written 4.1 years ago by
Kevin Blighe
87k
4
votes
0
replies
2.3k
views
Tutorial:
Exploring Encode Data In The Ucsc Genome Browser
encode
updated 14 months ago by
Ram
43k • written 11.7 years ago by
Mary
11k
4
votes
0
replies
765
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
0
replies
2.3k
views
Tutorial:
Accurate prediction of active enhancers using PARE
ChIP-Seq
histone-modification
enhancer
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Sachin Pundhir
▴ 100
4
votes
3
replies
4.6k
views
Tutorial:
How to get full taxonomy classification using taxize and myTAI
taxonomy
R
updated 13 months ago by
Ram
43k • written 6.0 years ago by
Daniel
★ 4.0k
4
votes
2
replies
2.5k
views
Tutorial:
Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0
beagle
updated 13 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
410 results • Page
5 of 9
Recent Votes
Read pair orientation : Illumina TruSeq Stranded mRNA library
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Interested in Spatial Omics?
Answer: Seurat merge and batch correction
Answer: Seurat merge and batch correction
Comment: Per base sequence content error in RNAseq analysis
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Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
b.contreras.moreira
▴ 170
This should work if you know your sequences are related, otherwise is safer to compute local alignments with BLAST
Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
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