From aec03edf006a09cfba9209192e0fce93cec96cf8 Mon Sep 17 00:00:00 2001 From: Obi Griffith Date: Mon, 13 Nov 2023 13:54:02 -0500 Subject: [PATCH] update links to updated lectures throughout --- _posts/0000-01-01-Intro_to_RNAseq.md | 4 ++-- _posts/0001-01-01-Intro_to_Inputs.md | 6 +++--- _posts/0001-02-01-Reference_Genomes.md | 2 +- _posts/0001-03-01-Annotations.md | 2 +- _posts/0001-04-01-Indexing.md | 2 +- _posts/0002-01-01-Intro_to_Alignment.md | 10 +++++----- _posts/0002-03-01-Alignment.md | 4 ++-- _posts/0002-06-01-Alignment_QC.md | 2 +- _posts/0003-01-01-Intro_to_Expression.md | 6 +++--- _posts/0003-02-01-Expression.md | 4 ++-- _posts/0003-03-01-Differential_Expression.md | 2 +- _posts/0004-01-01-Intro_to_Alignment_Free.md | 4 ++-- _posts/0004-02-01-Alignment_Free_Kallisto.md | 4 ++-- _posts/0005-01-01-Intro_to_Isoform_Analysis.md | 2 +- _posts/0009-04-01-Lectures.md | 9 +++++++++ 15 files changed, 36 insertions(+), 27 deletions(-) diff --git a/_posts/0000-01-01-Intro_to_RNAseq.md b/_posts/0000-01-01-Intro_to_RNAseq.md index 9fc12487..88bd7740 100644 --- a/_posts/0000-01-01-Intro_to_RNAseq.md +++ b/_posts/0000-01-01-Intro_to_RNAseq.md @@ -24,5 +24,5 @@ date: 0000-01-01 ### Lectures -* [Introduction to instructors](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/full/RNASeq_Module0_Introductions.pdf) -* [Introduction to cloud computing](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/full/RNASeq_Module0_CloudComputing.pdf) +* [Introduction to instructors](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/RNASeq_Module0_Introductions.pdf) +* [Introduction to cloud computing](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/RNASeq_Module0_CloudComputing.pdf) diff --git a/_posts/0001-01-01-Intro_to_Inputs.md b/_posts/0001-01-01-Intro_to_Inputs.md index f529e2af..39b6137c 100644 --- a/_posts/0001-01-01-Intro_to_Inputs.md +++ b/_posts/0001-01-01-Intro_to_Inputs.md @@ -23,6 +23,6 @@ date: 0001-01-01 ### Lecture -* [Introduction to RNA sequencing lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/full/RNASeq_Module1_IntrotoRNA.pdf) -* [FASTA/FASTQ/GTF formats mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_01_01_FASTA_FASTQ_GTF.pdf) -* [Indexing mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_01_02_Indexing.pdf) +* [Introduction to RNA sequencing lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/RNASeq_Module1_IntrotoRNA.pdf) +* [FASTA/FASTQ/GTF formats mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_01_01_FASTA_FASTQ_GTF.pdf) +* [Indexing mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_01_02_Indexing.pdf) diff --git a/_posts/0001-02-01-Reference_Genomes.md b/_posts/0001-02-01-Reference_Genomes.md index b8f6297c..cf96535f 100644 --- a/_posts/0001-02-01-Reference_Genomes.md +++ b/_posts/0001-02-01-Reference_Genomes.md @@ -16,7 +16,7 @@ date: 0001-02-01 *** ### FASTA/FASTQ/GTF mini lecture -If you would like a refresher on common file formats such as FASTA, FASTQ, and GTF files, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_01_01_FASTA_FASTQ_GTF.pdf) briefly covering these. +If you would like a refresher on common file formats such as FASTA, FASTQ, and GTF files, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_01_01_FASTA_FASTQ_GTF.pdf) briefly covering these. ### Obtain a reference genome from Ensembl, iGenomes, NCBI or UCSC. diff --git a/_posts/0001-03-01-Annotations.md b/_posts/0001-03-01-Annotations.md index 97f03b48..858dbcca 100644 --- a/_posts/0001-03-01-Annotations.md +++ b/_posts/0001-03-01-Annotations.md @@ -16,7 +16,7 @@ date: 0001-03-01 *** ### FASTA/FASTQ/GTF mini lecture -If you would like a refresher on common file formats such as FASTA, FASTQ, and GTF files, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_01_01_FASTA_FASTQ_GTF.pdf) briefly covering these. +If you would like a refresher on common file formats such as FASTA, FASTQ, and GTF files, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_01_01_FASTA_FASTQ_GTF.pdf) briefly covering these. ### Obtain Known Gene/Transcript Annotations diff --git a/_posts/0001-04-01-Indexing.md b/_posts/0001-04-01-Indexing.md index 86908c92..4dc46981 100644 --- a/_posts/0001-04-01-Indexing.md +++ b/_posts/0001-04-01-Indexing.md @@ -16,7 +16,7 @@ date: 0001-04-01 *** ### Indexing mini lecture -If you want a refresher on indexing, we have made an [indexing mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_01_02_Indexing.pdf) available. +If you want a refresher on indexing, we have made an [indexing mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_01_02_Indexing.pdf) available. ### Create a HISAT2 index Create a HISAT2 index for chr22 and the ERCC spike-in sequences. HISAT2 can incorporate exons and splice sites into the index file for alignment. First create a splice site file, then an exon file. Finally make the aligner FM index. diff --git a/_posts/0002-01-01-Intro_to_Alignment.md b/_posts/0002-01-01-Intro_to_Alignment.md index e3147703..ec4c3b4b 100644 --- a/_posts/0002-01-01-Intro_to_Alignment.md +++ b/_posts/0002-01-01-Intro_to_Alignment.md @@ -23,8 +23,8 @@ date: 0002-01-01 * BAM read counting and determination of variant allele expression status ### Lectures -* [Introduction to alignment mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_01_Alignment.pdf) -* [Alignment/Assembly/kmer mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf) -* [SAM/BAM/BED formats mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_03_SAM_BAM_BED.pdf) -* [Introduction to IGV lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/full/RNASeq_Module2_IGV_Tutorial_Brief.pdf) -* [Alignment QC mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_04_alignmentQC.pdf) +* [Introduction to alignment mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_01_Alignment.pdf) +* [Alignment/Assembly/kmer mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf) +* [SAM/BAM/BED formats mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_03_SAM_BAM_BED.pdf) +* [Introduction to IGV lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/RNASeq_Module2_IGV_Tutorial_Brief.pdf) +* [Alignment QC mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_04_alignmentQC.pdf) diff --git a/_posts/0002-03-01-Alignment.md b/_posts/0002-03-01-Alignment.md index 6ee0ca3e..b442dc70 100644 --- a/_posts/0002-03-01-Alignment.md +++ b/_posts/0002-03-01-Alignment.md @@ -10,9 +10,9 @@ date: 0002-03-01 --- ### Alignment mini lecture -If you would like a refresher on alignment, we have created an [alignment mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_01_Alignment.pdf). +If you would like a refresher on alignment, we have created an [alignment mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_01_Alignment.pdf). -We have also provided a mini lectures describing the differences between [alignment, assembly, and pseudoalignment](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf) and describing [sam, bam, and bed file formats](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_03_SAM_BAM_BED.pdf). +We have also provided a mini lectures describing the differences between [alignment, assembly, and pseudoalignment](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf) and describing [sam, bam, and bed file formats](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_03_SAM_BAM_BED.pdf). ### HISAT2 alignment Perform alignments with HISAT2 to the genome and transcriptome. diff --git a/_posts/0002-06-01-Alignment_QC.md b/_posts/0002-06-01-Alignment_QC.md index 442ca5ea..2839a107 100644 --- a/_posts/0002-06-01-Alignment_QC.md +++ b/_posts/0002-06-01-Alignment_QC.md @@ -16,7 +16,7 @@ date: 0002-06-01 *** ### Alignment QC mini lecture -If you would like a refresher on alignment QC, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_04_alignmentQC.pdf) briefly covering the topic. +If you would like a refresher on alignment QC, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_04_alignmentQC.pdf) briefly covering the topic. ### Use samtools and FastQC to evaluate the alignments Use `samtools view` to see the format of a SAM/BAM alignment file diff --git a/_posts/0003-01-01-Intro_to_Expression.md b/_posts/0003-01-01-Intro_to_Expression.md index 717d89af..cbb5c826 100644 --- a/_posts/0003-01-01-Intro_to_Expression.md +++ b/_posts/0003-01-01-Intro_to_Expression.md @@ -19,6 +19,6 @@ date: 0003-01-01 * Downstream interpretation of expression and differential estimates ### Lectures -* [Abundance Estimations lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_03_01_AbundanceEstimation.pdf) -* [HTSEQ lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_03_02_HTSEQ.pdf) -* [Differential expression lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_03_03_DifferentialExpression.pdf) +* [Abundance Estimations lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_03_01_AbundanceEstimation.pdf) +* [HTSEQ lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_03_02_HTSEQ.pdf) +* [Differential expression lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_03_03_DifferentialExpression.pdf) diff --git a/_posts/0003-02-01-Expression.md b/_posts/0003-02-01-Expression.md index e0a07961..78d802a5 100644 --- a/_posts/0003-02-01-Expression.md +++ b/_posts/0003-02-01-Expression.md @@ -16,7 +16,7 @@ date: 0003-02-01 *** ### Expression mini lecture -If you would like a refresher on expression and abundance estimations, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_03_01_AbundanceEstimation.pdf). +If you would like a refresher on expression and abundance estimations, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_03_01_AbundanceEstimation.pdf). ### Use Stringtie to generate expression estimates from the SAM/BAM files generated by HISAT2 in the previous module @@ -124,7 +124,7 @@ Solution: When you are ready you can check your approach against the [Solutions] #### Mini-lecture -For more on the differences between abundance estimates like FPKM and count data with HTSeq-count, see this [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_03_02_HTSEQ.pdf). +For more on the differences between abundance estimates like FPKM and count data with HTSeq-count, see this [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_03_02_HTSEQ.pdf). *** diff --git a/_posts/0003-03-01-Differential_Expression.md b/_posts/0003-03-01-Differential_Expression.md index 0eceec48..adb6baeb 100644 --- a/_posts/0003-03-01-Differential_Expression.md +++ b/_posts/0003-03-01-Differential_Expression.md @@ -17,7 +17,7 @@ date: 0003-03-01 ### Differential Expression mini lecture -If you would like a brief refresher on differential expression analysis, please refer to the [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_03_03_DifferentialExpression.pdf). +If you would like a brief refresher on differential expression analysis, please refer to the [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_03_03_DifferentialExpression.pdf). ### Ballgown DE Analysis diff --git a/_posts/0004-01-01-Intro_to_Alignment_Free.md b/_posts/0004-01-01-Intro_to_Alignment_Free.md index 782da327..a239c951 100644 --- a/_posts/0004-01-01-Intro_to_Alignment_Free.md +++ b/_posts/0004-01-01-Intro_to_Alignment_Free.md @@ -20,5 +20,5 @@ date: 0004-01-01 * Abundance estimation and differential expression analysis with Kallisto and Sleuth ### Lectures -* [Psuedo-alignment mini-lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_04_01_AlignmentFreeKallisto.pdf) -* [Differences between alignment, assembly, and pseudoalignment mini-lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf). +* [Psuedo-alignment mini-lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_04_01_AlignmentFreeKallisto.pdf) +* [Differences between alignment, assembly, and pseudoalignment mini-lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf). diff --git a/_posts/0004-02-01-Alignment_Free_Kallisto.md b/_posts/0004-02-01-Alignment_Free_Kallisto.md index d1819ea7..c2ebd375 100644 --- a/_posts/0004-02-01-Alignment_Free_Kallisto.md +++ b/_posts/0004-02-01-Alignment_Free_Kallisto.md @@ -11,8 +11,8 @@ date: 0004-02-01 ### Kallisto mini lecture -If you would like a refresher on Kallisto, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_04_01_AlignmentFreeKallisto.pdf) briefly covering the topic. -We have also made a mini lecture describing the differences between [alignment, assembly, and pseudoalignment](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf). +If you would like a refresher on Kallisto, we have made a [mini lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_04_01_AlignmentFreeKallisto.pdf) briefly covering the topic. +We have also made a mini lecture describing the differences between [alignment, assembly, and pseudoalignment](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_02_02_Alignment_vs_Assembly_vs_Kmer.pdf). *** diff --git a/_posts/0005-01-01-Intro_to_Isoform_Analysis.md b/_posts/0005-01-01-Intro_to_Isoform_Analysis.md index 08c374d7..04aeaad2 100644 --- a/_posts/0005-01-01-Intro_to_Isoform_Analysis.md +++ b/_posts/0005-01-01-Intro_to_Isoform_Analysis.md @@ -20,4 +20,4 @@ date: 0005-01-01 * Visualize junction counts and StringTie assembled transcripts in IGV ### Lecture -* [Alternative Splicing lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cbw/2023/mini/RNASeq_MiniLecture_05_01_AlternativeSplicingAnalysis.pdf) +* [Alternative Splicing lecture](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/mini/RNASeq_MiniLecture_05_01_AlternativeSplicingAnalysis.pdf) diff --git a/_posts/0009-04-01-Lectures.md b/_posts/0009-04-01-Lectures.md index 17526cd0..2c207444 100644 --- a/_posts/0009-04-01-Lectures.md +++ b/_posts/0009-04-01-Lectures.md @@ -20,6 +20,15 @@ date: 0009-04-01 * [2013 CBW course lectures](https://www.youtube.com/playlist?list=PL3izGL6oi0S_N63aEd9vLnFM3pNYt9NGQ) (YouTube) +### Advanced Sequencing Technologies & Bioinformatics Analysis (November 6-19, 2023) + +Organized by [Cold Spring Harbor Laboratory (CSHL)](http://www.cshl.edu/) - [Course Site](https://meetings.cshl.edu/courses.aspx?course=c-seqtec&year=23) + +**Presentations:** + +TBA + + ### CBW RNA-seq analysis (July 17-19th, 2023. Toronto, ON, Canada)) Organized by [Canadian Bioinformatics Workshops (CBW)](https://bioinformatics.ca/) - [Course Site](https://bioinformaticsdotca.github.io/RNA_2021)