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BAC module/readme.md

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+## Bacterial Artificial Chromosomes (BACs) Module 
+## (Human Disease Variant Discovery Module)
+
+### Objective
+
+The goal of this exercise is identify the gene and potential pathogenic genotypes (variants) in a series of BAC sequences on the platform of Galaxy.
+
+### Data background
+
+The Jackson Laboratory (JAX) acquired the anonymous Bacterial Artificial Chromosomes (BACs) human DNA fragments in order to engineer a humanized mouse model. The human genomic regions (~250 kb in size) were used to create transgenic mice that carry a large fragment of human chromosome 12. In order to attempt to duplicate the human disease in mice JAX has made a wide range of transgenic mice carrying numerous mutations found in humans; additionally the normal (non-mutation) region of human chromosome 12 has been engineered (inserted via transgenesis) into mice as a control. The BACs were prepared by library preparation and sequenced at JAX on an Illumina miSeq platform. Sequencing was done as paired-end with 150 bp reads. Sequencing ~250 kb is a small project by modern high throughput standards and by aligning to a single human chromosome during data analysis this module is computationally less demanding.
+
+### Obtain the sequence data
+
+All 24 fastq files (.fastq.gz) and a genome file (.fa) can be accessed at **ftp://ftp.jax.org/encode/BAC_Module** (copy and paste this address to your browser.) To fit the whole analysis into manageable time frame, the sequence files were already truncated to chromosome 1 (chr1).
+
+- 1_**S1**\_L001\_**R1**_001.fastq.gz: 1 = just #; S1 = experimental Sample1; L001 = Lane; R1 = Read 1 “forward read”; 001 = just #; fastq = file type
+- 1_**S1**\_L001\_**R2**_001.fastq.gz: The reverse reads paired with 1_S1_L001_R1_001.fastq.gz
+
+(Note: There are 12 paired-end reads. Each student or student group can or may work on one pair of reads.)
+
+- chr12.fa: A single fasta file for human chromosome 1, used for 	mapping reads as reference
+
+### Practice on [Galaxy](https://usegalaxy.org)
+
+Once you have all the sequence data, you are ready to proceed with RNA-seq analysis. Galaxy has all the tools and technical support. [UseGalaxy](https://usegalaxy.org) is open to everyone and allow you to work on datasets smaller than 250GB. Galaxy also provides other [options](https://galaxyproject.org/choices/) to meet diverse needs. 
+
+In this module, you need to
+1. Register an account on Galaxy if you haven't yet
+2. Open up the tutorial document '20180BAC ModuleSummary for Prof' (.docx or .pdf) and follow the steps