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News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 11 days ago by 3.0k • written 7.8 years ago by 101k
0
votes
0
replies
51
views
News: An Introduction to Nanopore direct RNA sequencing
cDNA Nanopore RNAseq
16 hours ago by carlopecoraro2 ★ 2.6k
1
vote
0
replies
137
views
News: Landscape Genomics course in Poland (January 20-24)
R LocalAdaptation Sambada LandscapeGenomics LFMM
2 days ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
120
views
News: Variant Analysis Online Course @ Edinburgh Genomics
variant-analysis online-training
updated 5 days ago by 44k • written 5 days ago by ▴ 40
0
votes
0
replies
166
views
News: online course - Metabolomics with R/Bioconductor
Metabolomics Bioconductor Multivariate-Data Untargeted Targeted
updated 7 days ago by 44k • written 7 days ago by ★ 2.6k
0
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0
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130
views
News: Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
low-coverage-WGS ANGSD Population-Genomics
updated 12 days ago by 44k • written 12 days ago by ★ 2.6k
0
votes
0
replies
191
views
News: Course: Introduction to CRISPR
GenomeEditing CRISPR Evolution
14 days ago by carlopecoraro2 ★ 2.6k
0
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0
replies
213
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News: Metabolomics with R/Bioconductor Online Course
Metabolomics Bioconductor R
updated 13 days ago by 44k • written 17 days ago by ★ 2.6k
0
votes
0
replies
211
views
News: Cellosaurus release 50 is available
database knowledgebase cell-line
updated 18 days ago by 44k • written 18 days ago by ▴ 120
0
votes
0
replies
172
views
News: Course: Metabarcoding in Microbial Ecology
R Qiime2 Metabarcoding Microbial-Ecology
19 days ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
242
views
News: Introduction to Nextflow course
Nextflow Pipeline Workflow-Manager Reproducibility
updated 20 days ago by 44k • written 21 days ago by ★ 2.6k
0
votes
0
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268
views
News: Beyond Beginner R: Advancing Your Coding Skills (Sept 16-19, 2024)
R Coding Reproducibility Programming
updated 23 days ago by 44k • written 23 days ago by ★ 2.6k
0
votes
0
replies
249
views
News: gnomAD v4 is now available on OpenCRAVAT!
gnomad Genomics OpenCRAVAT gnomADv4
updated 24 days ago by 44k • written 24 days ago by ▴ 10
0
votes
1
reply
272
views
News: ICOBLET 2024
Conference
updated 24 days ago by 145k • written 24 days ago by • 0
0
votes
0
replies
218
views
News: Join Our Online Course: Reproducibility Data Analysis with R (28-31 October 2024)
R Git Quarto Reproducibility Docker
24 days ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
126
views
News: ICOBLET 2024
Conference
25 days ago by mohamedsalahamine.benouar • 0
0
votes
0
replies
200
views
News: Course in Italy: Introduction to Statistics in R (30 September to 3 October 2024)
R GLM Statistics GLMM
4 weeks ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
177
views
News: Online course - Shotgun Metagenomics: Processing and Analysis
Prokka MetaPhlAn Metagenomics StrainPhlan PanPhlAn
updated 4 weeks ago by 44k • written 4 weeks ago by ★ 2.6k
1
vote
0
replies
155
views
News: RNAseq and Single Cell Analysis Online Courses @ Edinburgh Genomics
RNA-seq single-cell workshop
updated 4 weeks ago by 44k • written 4 weeks ago by ▴ 10
0
votes
0
replies
129
views
News: Phylogenomics course
Multispecies-Coalescent-Model Bayesian-Inference Phylogenomics Divergence-Time Maximum-Likelihood
updated 5 weeks ago by 44k • written 5 weeks ago by ★ 2.6k
1
vote
0
replies
228
views
News: Course - Machine Learning for Multi-Omics Integration
Machine-Learning Big-Data Multi-Omics Data-Integration Deep-Learning
updated 5 weeks ago by 44k • written 5 weeks ago by ★ 2.6k
0
votes
0
replies
215
views
News: Course: Introduction to Deep Learning
Deep-Learning Machine-Learning Python Convolutional-Neural-Network
6 days ago by carlopecoraro2 ★ 2.6k
3
votes
0
replies
164
views
News: Registration for the Nextflow Summit is still open. Get a 20% discount!
seqera nextflow
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 590
0
votes
0
replies
154
views
News: EMBO Practical Course Measuring translational dynamics by ribosome profiling
EMBORiboProf
5 weeks ago by EMBL Events ▴ 20
0
votes
0
replies
165
views
News: EMBL Conference The expanding world of RBPs: from posttranscriptional control to riboregulation
EMBLRBP
5 weeks ago by EMBL Events ▴ 20
1
vote
0
replies
150
views
News: EMBL Course Computing skills for reproducible research: software carpentry
EMBLSoftwareCarpentry
updated 5 weeks ago by 27k • written 5 weeks ago by ▴ 20
0
votes
0
replies
165
views
News: Course: Project Structure for Reproducible Work
workflows programming reproducibility replicability
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 10
0
votes
0
replies
154
views
News: Coding Courses @ Edinburgh Genomics
snakemake python R workshop linux
5 weeks ago by Kat @ EdGe ▴ 10
0
votes
0
replies
148
views
News: Course - Introduction to R Shiny
R Web-Applications Shiny
5 weeks ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
107
views
News: Course: Advance your Python Skills for Life Sciences
python vPython Pythonlang
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 70
0
votes
0
replies
96
views
News: Course: Introduction to R
Rproject Rlang Rstats
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 70
0
votes
0
replies
184
views
News: Course: Introduction to the Analysis of Longitudinal Data in Biology Using R
Longitudinal-Data R Epidemiology Forecasting Gene-Expression
updated 5 weeks ago by 44k • written 6 weeks ago by ★ 2.6k
0
votes
0
replies
195
views
News: Intro to Linux for Genomics Online Course
linux workshop genomics
updated 6 weeks ago by 44k • written 6 weeks ago by ▴ 10
0
votes
0
replies
131
views
News: Course: Structural Variant Detection and Comparison
Structural-Variants SVs Nanopore
6 weeks ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
147
views
News: Course: Transform your data into an interactive web app with R Shiny
Rshiny Dataviz Course
6 weeks ago by Transmitting Science communication ▴ 70
0
votes
0
replies
144
views
News: course on Generalized Linear Mixed Models in R
R Dharma Mixed-Models GLLM
6 weeks ago by carlopecoraro2 ★ 2.6k
1
vote
0
replies
153
views
News: Core_nt: new default database for NCBI nucleotide BLAST
core_nt NCBI blastn
6 weeks ago by EricS_NCBI ▴ 10
0
votes
0
replies
183
views
News: Check Out Our New Desktop App for scRNA-seq Data Analysis – Beta Testers Wanted!
scRNAseq
6 weeks ago by OmnibusX ▴ 90
0
votes
0
replies
185
views
News: Population Genomics course (online)
NGS PopulationGenomics Introgression LandscapeGenomics GWAS
7 weeks ago by carlopecoraro2 ★ 2.6k
0
votes
1
reply
209
views
News: A Practical Hands-On Introduction to R
Tidyverse R Data-Visualisation Data-Analysis ggplot2
updated 7 weeks ago by • 0 • written 7 weeks ago by ★ 2.6k
6
votes
2
replies
841
views
News: New more compact NCBI BLAST Core Nucleotide Database (core_nt) now available on the web
NCBI BLAST
updated 7 weeks ago by 145k • written 10 weeks ago by ▴ 510
0
votes
0
replies
149
views
News: Course - RNA-Seq Analyses in Non-Model Organisms (online)
Bioconductor Non-Model-Organisms Nanopore Pacbio RNA-seq
updated 7 weeks ago by 44k • written 7 weeks ago by ★ 2.6k
0
votes
0
replies
160
views
News: Online course on Reproducibility Data Analysis with R
R Github Git Reproducibility Docker
8 weeks ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
217
views
News: Online course: Genomic Data Visualization with R
Data-Visualisation Genomic-Data R
9 weeks ago by carlopecoraro2 ★ 2.6k
3
votes
0
replies
254
views
News: Now available for download: New, more efficient BLAST core_nt database
NCBI BLAST
9 weeks ago by PeterC_NCBI ▴ 510
4
votes
0
replies
325
views
News: Changes coming to NCBI Web blast in August 2024
nt core_nt blast NCBI WWWBLAST
10 weeks ago by GenoMax 145k
0
votes
0
replies
260
views
News: Online course: Metabolomics with R/Bioconductor (5th edition)
Metabolomics Bioconductor R
updated 10 weeks ago by 44k • written 11 weeks ago by ★ 2.6k
0
votes
0
replies
224
views
News: Online course: Introduction to Nextflow
Nextflow Pipeline Workflow-Manager Reproducibility
updated 11 weeks ago by 44k • written 11 weeks ago by ★ 2.6k
0
votes
0
replies
159
views
News: Course: RADseq data analysis using Stacks (online)
RAD-seq Genomics Stacks Phylogenomics Population
updated 11 weeks ago by 44k • written 11 weeks ago by ★ 2.6k
0
votes
0
replies
162
views
News: Virtual Genome Assembly Workshop 7/15-18
assembly workshop genome instruction virtual
11 weeks ago by mia.nahom ▴ 10
1,000 results • Page 1 of 20
Recent Votes
Answer: How to compile Multiz
Answer: Difference between GLM and Wilcoxon rank sum test
Answer: MarkDuplicatesSpark GATK flags for overcoming space issues
Answer: Numreads from samtools for Differential Expression
Comment: Numreads from samtools for Differential Expression
Answer: How to compile Multiz
C: How to make an intronic GTF for alignment
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Recent Replies
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz by GenoMax 145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz by Santex • 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
However, OE1_2 and OE1_3 are not the only groups experiencing problems. I tried another non-empty file, and: ``` rsem-calculate-expression …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
oops ``` file *.out.bam KO1_2Aligned.sortedByCoord.out.bam: gzip compressed data, extra field KO1_2Aligned.toTranscriptome.out.bam: …
Answer: Converting bam to sam using htslib C++ api by Pierre Lindenbaum 164k
read https://github.com/samtools/samtools/blob/develop/sam_view.c * allocate a new bam1_t* b = bam_init1 * open the input file: sam_op…
Comment: Converting bam to sam using htslib C++ api by Pierre Lindenbaum 164k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: FastQC and HISAT2 by Jaber • 0
Thank you, it worked almost after two months of struggle, I nearly deleted everything and reinstalled it, I assume the problem was someth…
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