Welcome to the VDR bioinformatics sessions!

We are starting on the 13th of October 2020 a series of bioinformatics sessions for the VDR lab members, covering the command line (bash) and several genomics techniques used in the lab!

Date	Session	Topic
13-Oct-2020	Session 1	Bash command line scripting + totoro + UCSC genome browser
20-Oct-2020	Session 2	ChIP-seq 1
27-Oct-2020	Session 3	ChIP-seq 2
3-Nov-2020	Session 4	ChIP-seq 3
10-Nov-2020	Session 5	ChIP-seq 4
17-Nov-2020	Session 6	ChIP-seq 5
30-Nov-2020	Session 7	ATAC-seq 1
15-Dec-2020	Session 8	ATAC-seq 2
12-Jan-2021	[Session 9]	ATAC-seq 3
19-Jan-2021	[Session 10]	[4C-seq 1]
26-Jan-2021	[Session 11]	[4C-seq 2]
2-Feb-2021	[Session 12]	[4C-seq 3]
9-Feb-2021	[Session 13]	[HiChIP-seq / HiC 1]
16-Feb-2021	[Session 14]	[HiChIP-seq / HiC 2]
23-Feb-2021	[Session 15]	[HiChIP-seq / HiC 3]
2-Mar-2021	[Session 16]	[RNA-seq 1]
9-Mar-2021	[Session 17]	[RNA-seq 2]
16-Mar-2021	[Session 18]	[RNA-seq 3]
23-Mar-2021	[Session 19]	Round-up / discussion

Doubts / Questions / Bugs: please add a new issue on ISSUES

Session 1

1. Bash command line scripting

Pre-course tutorial

More material: [Bash commands] [Shell filesystem] [grep+pipe] [for loops] [file permissions]

2. The i3S hpc unit: totoro

Totoro script template

-another example of HPC system

3. The UCSC genome browser: making a session and adding custom tracks

Sessions 2-6 - ChIP-seq

For processing in totoro, follow the step-by-step guide CommandLine_totoro_ChIPseq

Sessions 7-9 - ATAC-seq

For processing in totoro, follow the step-by-step guide ATACseq_commandLine_simple