update links to updated lectures throughout

griffithlab · Nov 13, 2023 · aec03ed · aec03ed
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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)