Difference between revisions of "RNA Seq on HPC"
| (3 intermediate revisions by the same user not shown) | |||
| Line 15: | Line 15: | ||
[[ 6. The tuxedo pipeline]] | [[ 6. The tuxedo pipeline]] | ||
| − | + | [[ 6.1 Genome indexing for bowtie ]] | |
| − | [[ 6.2 Read mapping using | + | [[ 6.2 Read mapping using tophat ]] |
[[ 6.3 Transcriptome reconstruction and expression using cufflinks ]] | [[ 6.3 Transcriptome reconstruction and expression using cufflinks ]] | ||
| Line 35: | Line 35: | ||
[[ 9. Using bwa for read mapping and SNP calling ]] | [[ 9. Using bwa for read mapping and SNP calling ]] | ||
| − | [[ 9.1 Genome indexing for | + | [[ 9.1 Genome indexing for bwa ]] |
| − | [[ 9.2 Read mapping using | + | [[ 9.2 Read mapping using bwa ]] |
[[ 9.3 SNP calling using varscan ]] | [[ 9.3 SNP calling using varscan ]] | ||
[[ 10. Useful references ]] | [[ 10. Useful references ]] | ||
Latest revision as of 15:32, 20 February 2016
The following Hands-on tutorial is based on the EBI teaching materials from Myrto Kostadima and Remco Loos at https://www.ebi.ac.uk/training/online/
6.1 Genome indexing for bowtie
6.3 Transcriptome reconstruction and expression using cufflinks
6.4 Differential Expression using cuffdiff
7. Using STAR for read mapping
7.3 Using cuffdiff on STAR mapped reads
8. De novo assembly with Velvet
