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Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
11 minutes ago by GenoMax 136k
5
votes
2
replies
2.2k
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 8 months ago by 41k • written 4.8 years ago by ▴ 10
15
votes
2
replies
2.9k
views
Tutorial: Introduction to bedtools.
bedtools
updated 8 months ago by 41k • written 9.0 years ago by 12k
4
votes
2
replies
3.5k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 8 months ago by 41k • written 7.8 years ago by ★ 2.5k
1
vote
2
replies
3.2k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 13 months ago by 41k • written 8.3 years ago by ▴ 10
60
votes
2
replies
7.2k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
7
votes
2
replies
3.4k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 9 months ago by 41k • written 11.1 years ago by 11k
3
votes
2
replies
2.5k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 6 months ago by 41k • written 6.6 years ago by ▴ 100
6
votes
2
replies
2.6k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 9 months ago by 41k • written 9.8 years ago by ▴ 610
9
votes
2
replies
5.3k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 7 months ago by 41k • written 7.5 years ago by ▴ 140
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 16 months ago by 41k • written 7.8 years ago by ★ 1.8k
15
votes
2
replies
6.7k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 9 months ago by 41k • written 11.3 years ago by 99k
19
votes
2
replies
3.3k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 6 months ago by 41k • written 6.6 years ago by ▴ 640
4
votes
2
replies
2.5k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 12 weeks ago by 136k • written 3.6 years ago by 78k
5
votes
2
replies
695
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 3 months ago by 41k • written 3 months ago by ★ 2.4k
10
votes
2
replies
3.3k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 15 months ago by 41k • written 8.0 years ago by 20k
5
votes
2
replies
2.2k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 8 months ago by 41k • written 5.0 years ago by ▴ 50
15
votes
2
replies
3.6k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
12
votes
2
replies
1.2k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 8 months ago by 41k • written 2.7 years ago by 12k
11
votes
1
reply
2.5k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 8 months ago by 41k • written 2.9 years ago by ★ 25k
22
votes
1
reply
3.1k
views
Tutorial: Introduction To R Course Materials Available
R
updated 11 months ago by 41k • written 11.6 years ago by 26k
0
votes
1
reply
1.8k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
12
votes
1
reply
4.9k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 13 months ago by 41k • written 8.3 years ago by 3.5k
0
votes
1
reply
3.0k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 6 months ago by 41k • written 6.1 years ago by • 0
0
votes
1
reply
319
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 11 weeks ago by 78k • written 11 weeks ago by ▴ 30
0
votes
1
reply
988
views
Tutorial: Add Customized Filters in GDC
gdc
updated 2.5 years ago by 21k • written 2.5 years ago by ★ 1.1k
10
votes
1
reply
2.2k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 8 months ago by 41k • written 3.7 years ago by ★ 2.5k
13
votes
1
reply
2.7k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.5 years ago by ★ 16k • written 2.5 years ago by 86k
1
vote
1
reply
1.8k
views
Tutorial: Live webinar: Implications of Next Generation Sequencing in Molecular Diagnosis of Cancer on 28 Sep 2016
alignment sequencing genome SNP
updated 7 months ago by 41k • written 7.3 years ago by ▴ 70
2
votes
1
reply
2.9k
views
Tutorial: Scripting for Biology - Online Virtual Classroom-based Module
perl python GO class
updated 14 months ago by 41k • written 8.3 years ago by ★ 1.1k
15
votes
1
reply
3.5k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 15 months ago by ★ 1.8k • written 23 months ago by 14k
0
votes
1
reply
2.1k
views
Tutorial: From Genefiltering to Results storgae in Microarray Analysis using in R (Part II) - FARMS
gene R
updated 7 months ago by 41k • written 7.5 years ago by ▴ 140
2
votes
1
reply
2.9k
views
Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 8 months ago by 41k • written 3.8 years ago by ▴ 10
4
votes
1
reply
1.8k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 6 months ago by 41k • written 6.3 years ago by ▴ 40
2
votes
1
reply
1.9k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 10 months ago by 158k • written 10 months ago by ★ 2.0k
3
votes
1
reply
2.2k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 6 months ago by 41k • written 6.5 years ago by ★ 1.6k
15
votes
1
reply
3.1k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 7 months ago by 41k • written 7.6 years ago by 19k
1
vote
1
reply
1.3k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 8 months ago by 41k • written 3.3 years ago by • 0
0
votes
1
reply
1.3k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 8 months ago by 41k • written 5.8 years ago by ▴ 10
7
votes
1
reply
1.9k
views
Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 8 months ago by 41k • written 8.4 years ago by ▴ 410
10
votes
1
reply
8.6k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 6 months ago by 41k • written 6.2 years ago by ▴ 110
7
votes
1
reply
2.2k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 6 months ago by 41k • written 6.1 years ago by ★ 1.7k
5
votes
1
reply
2.4k
views
Tutorial: Nice simple interactive Vim tutorial
vim linux
updated 8 months ago by 41k • written 9.1 years ago by 9.7k
2
votes
1
reply
49k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 16 months ago by 3.8k • written 16 months ago by ▴ 20
6
votes
1
reply
2.9k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 9 months ago by 41k • written 9.6 years ago by ▴ 220
8
votes
1
reply
1.3k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 8 months ago by 41k • written 2.7 years ago by 86k
0
votes
1
reply
2.8k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 8 months ago by 41k • written 5.3 years ago by ▴ 320
15
votes
1
reply
6.8k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.0k
0
votes
1
reply
2.6k
views
Tutorial: Clustering and results Display from PART II (PART III) - MeV software version
gene R
updated 7 months ago by 41k • written 7.5 years ago by ▴ 140
4
votes
1
reply
3.1k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 9 months ago by 41k • written 11.6 years ago by ▴ 360
383 results • Page 5 of 8
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Popular Question to endre.sebestyen ▴ 10
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Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by GenoMax 136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by Brian Bushnell 19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters? by AMARU • 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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