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  1. 1.1 RNA-Seq analysis tools
  2. 1. Introduction
  3. 1. Read Quality Assessment
  4. 10. Useful references
  5. 2. Quality trimming
  6. 2. Your environment
  7. 26th July 2013
  8. 3.Identification and masking of repeat elements
  9. 3. Running Trinity
  10. 3. Your data
  11. 3. Your environment
  12. 4.Identification and masking of repeat elements
  13. 4. Evaluating the assembly
  14. 4. Quality control
  15. 4. Your data
  16. 5.Identification and masking of repeat elements
  17. 5. Transcript expression quantitation
  18. 5. Trimming
  19. 6.1 Genome indexing for bowtie
  20. 6.2 Read mapping using tophat
  21. 6.3 Transcriptome reconstruction and expression using cufflinks
  22. 6.4 Differential Expression using cuffdiff
  23. 6. Construct an expression matrix
  24. 6. The tuxedo pipeline
  25. 7. Evaluating the assembly with ExN50
  26. 7. Using STAR for read mapping
  27. 8. De novo assembly with Velvet
  28. 8. Expression analysis
  29. 9.1 Genome indexing for bwa
  30. 9.2 Read mapping using bwa
  31. 9.3 SNP calling using varscan
  32. 9. Using bwa for read mapping and SNP calling
  33. ABySS
  34. Active Perl
  35. Array jobs
  36. Asking for Help
  37. Available Software
  38. Bert and Ernie - An Overview
  39. Blast
  40. Blast2go
  41. Complex submissions
  42. Convert fasta to 1l fasta.sh
  43. Diamond Blast
  44. Filezilla
  45. Genome Annotation
  46. Getting an account
  47. Installing your own modules
  48. Intermittent login failures on the HPC and some VMs
  49. Java memory allocation issues
  50. Main Page
  51. Matlab
  52. Meeting minutes
  53. MobaXterm
  54. Module Environment
  55. Monitoring your jobs
  56. Nodes, Cores, Slots
  57. OrthoMCL
  58. Orthomcl.config
  59. Progressive Cactus
  60. Putty
  61. Quick start
  62. RNA Seq on HPC
  63. RNA Seq on HPC (using Trinity)
  64. Running BLAST optimally
  65. SCW Access Procedures
  66. SCW Introduction
  67. SCW Training Materials
  68. SPRINT
  69. Scheduling and queuing
  70. Singularity Containers
  71. Split multifasta.pl
  72. Splitting Multifastas
  73. Submitting your job using Slurm
  74. UNIX Graphical interface
  75. Use scratch space
  76. VPN and SSH via central
  77. What is a HPC
  78. Your disk space

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