User contributions
- 16:27, 6 March 2017 (diff | hist) . . (+164) . . 8. Expression analysis (current)
- 16:24, 6 March 2017 (diff | hist) . . (+7,669) . . 8. Expression analysis
- 16:01, 6 March 2017 (diff | hist) . . (+1,300) . . N 8. Expression analysis (Created page with "A plethora of tools are currently available for identifying differentially expressed transcripts based on RNA-Seq data, and of these, edgeR and DESeq2 are very popular and hig...")
- 15:53, 6 March 2017 (diff | hist) . . (+2,014) . . N 7. Evaluating the assembly with ExN50 (Created page with "Below is described the use of an alternative statistic - the ExN50 value, which you assert is more useful in assessing the quality of the transcriptome assembly. The ExN50 ind...") (current)
- 15:42, 6 March 2017 (diff | hist) . . (+2,229) . . 6. Construct an expression matrix (current)
- 15:32, 6 March 2017 (diff | hist) . . (-11) . . 6. Construct an expression matrix
- 15:31, 6 March 2017 (diff | hist) . . (+2,105) . . N 6. Construct an expression matrix (Created page with "Now, given the expression estimates for each of the transcripts in each of the samples, you're going to pull together expression values into matrices containing transcript IDs...")
- 15:17, 6 March 2017 (diff | hist) . . (+2,259) . . 5. Transcript expression quantitation (current)
- 15:09, 6 March 2017 (diff | hist) . . (+1,693) . . 5. Transcript expression quantitation
- 15:02, 6 March 2017 (diff | hist) . . (+1,673) . . N 5. Transcript expression quantitation (Created page with "'''Abundance estimation using RSEM''' To estimate the expression levels of the Trinity-reconstructed transcripts, you can use the strategy supported by the RSEM software invo...")
- 14:50, 6 March 2017 (diff | hist) . . (+3) . . RNA Seq on HPC (using Trinity) (current)
- 14:50, 6 March 2017 (diff | hist) . . (+465) . . 4. Evaluating the assembly (current)
- 14:49, 6 March 2017 (diff | hist) . . (+773) . . 4. Evaluating the assembly
- 14:45, 6 March 2017 (diff | hist) . . (+55) . . 3. Running Trinity (current)
- 14:44, 6 March 2017 (diff | hist) . . (+1,315) . . 4. Evaluating the assembly
- 14:37, 6 March 2017 (diff | hist) . . (+225) . . N 4. Evaluating the assembly (Created page with "There are several ways to quantitatively as well as qualitatively assess the overall quality of the assembly. Check Trinity wiki [https://github.com/trinityrnaseq/trinityrnase...")
- 14:34, 6 March 2017 (diff | hist) . . (+181) . . 3. Running Trinity
- 14:33, 6 March 2017 (diff | hist) . . (+8) . . 3. Running Trinity
- 14:32, 6 March 2017 (diff | hist) . . (+1,243) . . N 3. Running Trinity (Created page with "In silico read normalisation: Large rna-seq data sets will have a large excess of reads corresponding to moderately and highly expressed transcripts, and these are far more t...")
- 14:28, 6 March 2017 (diff | hist) . . (-39) . . RNA Seq on HPC (using Trinity)
- 14:24, 6 March 2017 (diff | hist) . . (+182) . . 2. Quality trimming (current)
- 14:23, 6 March 2017 (diff | hist) . . (0) . . 2. Quality trimming
- 14:22, 6 March 2017 (diff | hist) . . (+191) . . 2. Quality trimming
- 14:19, 6 March 2017 (diff | hist) . . (-72) . . 2. Quality trimming
- 14:17, 6 March 2017 (diff | hist) . . (+3) . . 2. Quality trimming
- 14:14, 6 March 2017 (diff | hist) . . (+13) . . 2. Quality trimming
- 14:14, 6 March 2017 (diff | hist) . . (+1,272) . . N 2. Quality trimming (Created page with "In the event that quality trimming is required, we recommend using the Trimmomatic software. According to MacManes (2014), light trimming of reads at or below Phred=5 scores c...")
- 14:11, 6 March 2017 (diff | hist) . . (-2) . . 1. Read Quality Assessment (current)
- 14:10, 6 March 2017 (diff | hist) . . (+29) . . 1. Read Quality Assessment
- 14:10, 6 March 2017 (diff | hist) . . (+150) . . 1. Read Quality Assessment
- 14:08, 6 March 2017 (diff | hist) . . (+252) . . N 1. Read Quality Assessment (Created page with "Running FASTQC on the raw reads: #$ -S /bin/sh #$ -cwd ##$ -q amd.q,large.q,intel.q ##$ -l h_vmem=40G module load fastqc/0.11.2 FILES=/ibers/ernie/scratch/userName/Fa...")
- 14:04, 6 March 2017 (diff | hist) . . (+283) . . RNA Seq on HPC (using Trinity)
- 13:59, 6 March 2017 (diff | hist) . . (+32) . . N RNA Seq on HPC (using Trinity) (Created page with " 1. Read Quality Assessment ")
- 16:02, 19 January 2017 (diff | hist) . . (+36) . . Main Page (→Tutorials)
- 16:00, 19 January 2017 (diff | hist) . . (-51) . . Main Page
- 15:57, 19 January 2017 (diff | hist) . . (-1) . . Main Page (Undo revision 53987 by Val1 (talk))
- 15:53, 19 January 2017 (diff | hist) . . (+1) . . Main Page (→Tutorials)
- 15:52, 19 January 2017 (diff | hist) . . (+1) . . Main Page (→Tutorials)
- 15:52, 19 January 2017 (diff | hist) . . (+50) . . Main Page (→Tutorials)