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325 results • Page 4 of 7
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5
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0
replies
4.1k
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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
updated 6 months ago by 40k • written 2.7 years ago by 134k
5
votes
1
reply
4.0k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 9 months ago by 40k • written 8.3 years ago by 7.9k
5
votes
3
replies
4.0k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 7 months ago by 40k • written 10.8 years ago by ▴ 80
9
votes
3
replies
4.0k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 7 months ago by 40k • written 11.1 years ago by 98k
9
votes
4
replies
4.0k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
6 weeks ago by Hamid Ghaedi 3.0k
9
votes
9
replies
3.9k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 4 months ago by 40k • written 6.0 years ago by 86k
6
votes
2
replies
3.9k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 4 months ago by 40k • written 6.3 years ago by ★ 1.6k
10
votes
0
replies
3.8k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 6 months ago by 40k • written 2.7 years ago by 134k
6
votes
2
replies
3.6k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 5 months ago by 40k • written 7.5 years ago by ▴ 840
3
votes
2
replies
3.6k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 4 months ago by 40k • written 6.5 years ago by ▴ 30
3
votes
1
reply
3.6k
views
Tutorial: Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene R
updated 5 months ago by 40k • written 7.3 years ago by ▴ 140
20
votes
14
replies
3.6k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 5 months ago by 40k • written 7.4 years ago by ▴ 460
10
votes
2
replies
3.5k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 4 months ago by 40k • written 6.5 years ago by 26k
3
votes
0
replies
3.5k
views
Tutorial: Video Tutorial On Conducting Whole-Exome Sequencing Research
exome-sequencing
updated 7 months ago by 40k • written 10.3 years ago by 9.7k
6
votes
0
replies
3.5k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 6 months ago by 40k • written 9.3 years ago by 7.9k
0
votes
0
replies
3.5k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 4 months ago by 40k • written 5.6 years ago by ▴ 10
0
votes
0
replies
3.5k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 4 months ago by 40k • written 5.7 years ago by ▴ 10
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 4 months ago by 40k • written 4.9 years ago by ▴ 340
15
votes
2
replies
3.4k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
4
votes
2
replies
3.4k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 6 months ago by 40k • written 7.6 years ago by ★ 2.4k
7
votes
2
replies
3.4k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 7 months ago by 40k • written 11.0 years ago by 11k
3
votes
0
replies
3.3k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 6 months ago by 40k • written 3.2 years ago by 8.2k
10
votes
4
replies
3.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 4 months ago by 40k • written 5.6 years ago by 86k
19
votes
2
replies
3.2k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 4 months ago by 40k • written 6.5 years ago by ▴ 640
7
votes
8
replies
3.2k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 9 months ago by 40k • written 8.2 years ago by ★ 2.2k
1
vote
4
replies
3.1k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 4 months ago by 40k • written 5.4 years ago by ▴ 340
1
vote
4
replies
3.1k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
1
vote
2
replies
3.1k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 11 months ago by 40k • written 8.2 years ago by ▴ 10
4
votes
1
reply
3.1k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 7 months ago by 40k • written 11.4 years ago by ▴ 360
6
votes
0
replies
3.1k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 7 months ago by 40k • written 11.4 years ago by 26k
22
votes
1
reply
3.1k
views
Tutorial: Introduction To R Course Materials Available
R
updated 8 months ago by 40k • written 11.4 years ago by 26k
2
votes
0
replies
3.0k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 3 months ago by 40k • written 5.9 years ago by ★ 2.4k
15
votes
1
reply
3.0k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 5 months ago by 40k • written 7.4 years ago by 19k
1
vote
3
replies
3.0k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 5 months ago by 40k • written 7.1 years ago by ▴ 300
5
votes
0
replies
3.0k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 6 months ago by 40k • written 3.6 years ago by ★ 3.3k
0
votes
1
reply
3.0k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 4 months ago by 40k • written 5.9 years ago by • 0
7
votes
14
replies
3.0k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 11 months ago by • 0 • written 19 months ago by ▴ 30
5
votes
2
replies
3.0k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 4 months ago by 40k • written 6.5 years ago by ★ 9.3k
0
votes
0
replies
2.9k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 4 months ago by 40k • written 5.8 years ago by ▴ 10
2
votes
6
replies
2.9k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 5 months ago by 40k • written 7.2 years ago by ▴ 140
7
votes
0
replies
2.9k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 5 months ago by 40k • written 7.4 years ago by ★ 5.1k
6
votes
1
reply
2.9k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 6 months ago by 40k • written 9.4 years ago by ▴ 220
2
votes
1
reply
2.9k
views
Tutorial: Scripting for Biology - Online Virtual Classroom-based Module
perl python GO class
updated 12 months ago by 40k • written 8.1 years ago by ★ 1.1k
15
votes
2
replies
2.8k
views
Tutorial: Introduction to bedtools.
bedtools
updated 6 months ago by 40k • written 8.9 years ago by 12k
2
votes
1
reply
2.8k
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 6 months ago by 40k • written 3.6 years ago by ▴ 10
2
votes
0
replies
2.7k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 10 weeks ago by 40k • written 10 weeks ago by ★ 3.4k
0
votes
0
replies
2.7k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 4 months ago by 40k • written 5.8 years ago by ▴ 10
0
votes
1
reply
2.7k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 6 months ago by 40k • written 5.1 years ago by ▴ 310
0
votes
1
reply
2.6k
views
Tutorial: Clustering and results Display from PART II (PART III) - MeV software version
gene R
updated 5 months ago by 40k • written 7.3 years ago by ▴ 140
6
votes
2
replies
2.5k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 6 months ago by 40k • written 9.7 years ago by ▴ 610
325 results • Page 4 of 7
Recent Votes
Answer: Fetch Fastq files directly for SRA data
Answer: Running Rockhopper from a command-line
Comment: Hisat2 index and alignment question
Comment: How the first sequencing template removed in pair end sequencing
Comment: Which function is best for pathway analysis?
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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Recent Awards • All
Voter to rfran010 ▴ 810
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Recent Replies
Comment: identify DEGs across all conditions and per specific conditions by luffy ▴ 50
@camillab, Please look into Kevin Blighe's response in this [post][1] hope that helps. [1]: https://www.biostars.org/p/357464/
Answer: Running Rockhopper from a command-line by langziv ▴ 50
I managed to resolve the issue by passing absolute paths instead of relative ones.
Comment: Which function is best for pathway analysis? by luffy ▴ 50
@chris Please look into @Hamid Ghaedi's well documented [post][1] on ORA and GSEA, Or [this][2] documentation. Hope this helps. [1]: ht…
Comment: Bacterial Pangenome Analysis by kirankumareripogu ▴ 10
Hi @liorglic, Thank you for your prompt response. I totally agree with you that different blastp cuttoffs provide different results and…
Answer: Fetch Fastq files directly for SRA data by Rob 6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe by YUYANG.OON • 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject by Qi • 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis? by Yogi ▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions by Yogi ▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question by Istvan Albert 98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate by dsull ★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
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