Fix spelling and urls

09a-WGS-and-WXS.Rmd

@@ -57,7 +57,7 @@ For WXS or other targeted sequencing specifically (so not relevant to WGS data),
 
     - [Hybridization based enrichment](https://www.paragongenomics.com/target-enrichment/). This includes a variety of widely used methods that we will broadly categorize in two groups: Array-based and In-solution:
       - [Array-based capture](https://en.wikipedia.org/wiki/Exome_sequencing#:~:text=Target%2Denrichment%20strategies-,Array%2Dbased%20capture,-In%2Dsolution%20capture) uses microarrays that have probes designed to bind to known coding sequences. Fragments that do not bind to these probes are washed away, leaving the sample with known coding sequences bound and ready for PCR amplification [@Hodges2007; @Turner2009].
-      - [In-solution capture](https://en.wikipedia.org/wiki/Exome_sequencing#In-solution_capture) has become more popular in recent years because it [requires less sample DNA than array-base capture](https://sequencing.roche.com/global/en/article-listing/what-is-ngs-target-enrichment-and-why-is-it-important.html). To enrich for coding sequences, in-solution capture has a pool of custom probes that are designed to bind to the coding regions in the sample. Attached to these probes are beads which can be physically separated from DNA that is not bound to the probes (this should be the non-coding sequences) [@Mamanova2010].  
+      - [In-solution capture](https://en.wikipedia.org/wiki/Exome_sequencing#In-solution_capture) has become more popular in recent years because it [requires less sample DNA than array-base capture](https://www.illumina.com/techniques/sequencing/dna-sequencing/targeted-resequencing/target-enrichment.html). To enrich for coding sequences, in-solution capture has a pool of custom probes that are designed to bind to the coding regions in the sample. Attached to these probes are beads which can be physically separated from DNA that is not bound to the probes (this should be the non-coding sequences) [@Mamanova2010].  
     - [PCR/Amplicon based enrichment](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9318977/) requires even less sample than the other two strategies and so is ideal for when the amount of sample is limited or the DNA has been otherwise processed harshly (e.g. with paraffin embedding). Because the other two enrichment methods are done after PCR amplification has been done to the whole genomic DNA sample, its thought that this method of selective PCR amplification for enrichment can result in more uniformly amplified DNA in the resulting sample. However this is less suitable the more gene targets you have (like if you truly need to sequence all of the exome) since amplicons need to be designed for each target. Overall it is much more affordable of a method. There are several variations of this method that are [discussed thoroughly by @Singh2022](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9318977/).
 
 ## DNA Sequencing Pipeline Overview

11a-ATAC-Seq.Rmd

@@ -255,7 +255,7 @@ This section has been written by AI and needs verification by experts. This is m
 ## More resources about ATAC-seq data
 
 - [ATAC-seq overview from Galaxy](https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/slides.html#1) - these slides explain the overarching concepts of ATAC-seq.
-- [ATAC seq guidelines from Harvard](https://informatics.fas.harvard.edu/atac-seq-guidelines.html) - this workflow runs through step by step how to analysis ATAC-seq data and what different parameters mean.
+- [ATAC seq guidelines from ENCODE](https://www.encodeproject.org/atac-seq/) - this step by step overview covers ATAC-seq workflow and considerations.
 - [ATAC-seq review](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1929-3) - this paper gives a great overview of ATAC-seq data and step by step what needs to be considered.
 - [Identifying and mitigating bias in chromatin](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4473780/)
 - [CHIP Snakemake pipeline for analyzing ChIP-seq and chromatin accessibility data](https://f1000research.com/articles/10-517)

11c-ChIP-Seq.Rmd

@@ -139,7 +139,7 @@ Annotation
 - [EnrichedHeatmap](https://bioconductor.org/packages/release/bioc/html/EnrichedHeatmap.html)is an R package for making heatmaps that visualize the enrichment of genomic signals on specific target regions.
 - [SeqMonk](https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) is a software package designed for the visualization and analysis of large-scale genomic data. It includes a heatmap function that can generate heatmaps from ChIP-seq data.
 - [ngs.plot](https://github.com/shenlab-sinai/ngsplot) is a tool that can generate different types of plots, including heatmaps, from NGS data. It includes a ChIP-seq specific mode that can be used to generate heatmaps from ChIP-seq data.
-- [ChAsE: ChAsE (ChIP-seq Analysis Engine)](http://chase.cs.univie.ac.at/overview) is a web-based platform for ChIP-seq analysis that includes a heatmap function that can generate heatmaps from ChIP-seq data.
+- [ChAsE: ChAsE (ChIP-seq Analysis Engine)](https://github.com/hyounesy/ChAsE/) is a web-based platform for ChIP-seq analysis that includes a heatmap function that can generate heatmaps from ChIP-seq data.
 
 These tools allow users to generate heatmaps of ChIP-seq data, which can be used to identify enriched regions of binding and to visualize patterns of binding across genomic regions.
 

11d-CUT-and-RUN.Rmd

@@ -48,7 +48,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1YwxXy2rnUgbx_7B7
 
 ### CUT&RUN
 
-**Cleavage Under Targets and Release Using Nuclease**, **CUT&RUN** for short, is an antibody-targeted chromatin profiling method to measure the histone modification enrichment or transcription factor binding. This is a more advanced technology for epigenomic landscape profiling compared to the tradditional ChIP-seq technology and known for its easy implementation and low cost.  The procedure is carried out in situ where micrococcal nuclease tethered to protein A binds to an antibody of choice and cuts immediately adjacent DNA, releasing DNA-bound to the antibody target. Therefore, CUT&RUN produces precise transcription factor or histone modification profiles while avoiding crosslinking and solubilization issues. Extremely low backgrounds make profiling possible with typically one-tenth of the sequencing depth required for ChIP-seq and permit profiling using low cell numbers (i.e., a few hundred cells) without losing quality.
+**Cleavage Under Targets and Release Using Nuclease**, **CUT&RUN** for short, is an antibody-targeted chromatin profiling method to measure the histone modification enrichment or transcription factor binding. This is a more advanced technology for epigenomic landscape profiling compared to the traditional ChIP-seq technology and known for its easy implementation and low cost.  The procedure is carried out in situ where micrococcal nuclease tethered to protein A binds to an antibody of choice and cuts immediately adjacent DNA, releasing DNA-bound to the antibody target. Therefore, CUT&RUN produces precise transcription factor or histone modification profiles while avoiding crosslinking and solubilization issues. Extremely low backgrounds make profiling possible with typically one-tenth of the sequencing depth required for ChIP-seq and permit profiling using low cell numbers (i.e., a few hundred cells) without losing quality.
 
 <!-- [Henikoff lab](https://research.fredhutch.org/henikoff/en.html) constructed a 6xHis and HA-tagged protein A-protein G-MNase fusion (pAG-MNase) that allows direct binding of mouse antibodies that bind poorly to protein A, eliminating the need for a secondary antibody. The His tag allows the purification of pAG-MNase with a commercial kit, while the HA tag can be used for pulling out pAG-MNase chromatin complexes for CUT&RUN.ChIP. Henikoff lab developed low salt and high calcium conditions that prevent diffusion of released complexes into the supernatant, allowing for longer digestion times and increased yields without increased cleavage at non-specific accessible sites. E. coli DNA carried over from pA-MNase or pAG-MNase preparation is sufficient for internal calibration of samples without adding heterologous spike-in DNA. -->
 
@@ -81,7 +81,7 @@ CUT&RUN has been automated using a Beckman Biomek FX liquid-handling robot so th
 
 ### CUT&Tag
 
-**Cleavage Under Targets and Tagmentation**, **CUT&Tag** for short, is an enzyme tethering approach to profiling chromatin proteins, including histone marks and RNA Pol II. CUT&Tag generates sequence-ready libraries without the need for end polishing and adaptor ligation. It uses a proteinA-Tn5 fusion to tether Tn5 transposase near the site of an antibody to a chromatin protein of interest. A secondary antibody, such as guinea pig anti-rabbit antibody, is used to increase the efficiency of tethering the pA-Tn5 to the target primary antibody. The pA-Tn5 complex is pre-loaded with sequencing adapters that insert into adjacent DNA upon activation with magnesium. CUT&Tag has a very low background and can be performed in a single tube in as little as a day, though primary antibodies are typically incubated overnight. It can also be used with the ICELL8 nano dispensation system to profile single cells.
+**Cleavage Under Targets and Tagmentation**, **CUT&Tag** for short, is an enzyme tethering approach to profiling chromatin proteins, including histone marks and RNA Pol II. CUT&Tag generates sequence-ready libraries without the need for end polishing and adapter ligation. It uses a proteinA-Tn5 fusion to tether Tn5 transposase near the site of an antibody to a chromatin protein of interest. A secondary antibody, such as guinea pig anti-rabbit antibody, is used to increase the efficiency of tethering the pA-Tn5 to the target primary antibody. The pA-Tn5 complex is pre-loaded with sequencing adapters that insert into adjacent DNA upon activation with magnesium. CUT&Tag has a very low background and can be performed in a single tube in as little as a day, though primary antibodies are typically incubated overnight. It can also be used with the ICELL8 nano dispensation system to profile single cells.
 
 A streamlined CUT&Tag protocol was introduced by the [Henikoff Lab](https://research.fredhutch.org/henikoff/en.html) that suppresses DNA accessibility artifacts to ensure high-fidelity mapping of the antibody-targeted protein and improves the signal-to-noise ratio over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube, from cells to amplified libraries, providing low-cost genome-wide chromatin maps. By simplifying library preparation, CUT&Tag-direct requires less than a day at the bench, from live cells to sequencing-ready barcoded libraries. As a result of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for as little as $25 per sample. This enables routine genome-wide profiling of chromatin proteins and modifications and requires no special skills or equipment.