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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. Bert and Ernie - An Overview
  38. Blast2go
  39. Convert fasta to 1l fasta.sh
  40. Diamond Blast
  41. Filezilla
  42. Getting an account
  43. Installing your own modules
  44. Intermittent login failures on the HPC and some VMs
  45. Java memory allocation issues
  46. Matlab
  47. MobaXterm
  48. Module Environment
  49. Monitoring your jobs
  50. Nodes, Cores, Slots

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