Difference between revisions of "RNA Seq on HPC"
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− | [[ 1. | + | [[ 1. Introduction ]] |
[[ 1.1 RNA-Seq analysis tools ]] | [[ 1.1 RNA-Seq analysis tools ]] | ||
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[[ 6.4 Differential Expression using cuffdiff ]] | [[ 6.4 Differential Expression using cuffdiff ]] | ||
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+ | [[ 7. Using STAR for read mapping ]] | ||
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+ | [[ 7.1 Genome indexing for STAR ]] | ||
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+ | [[ 7.2 Read mapping using STAR ]] | ||
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+ | [[ 7.3 Using cuffdiff on STAR mapped reads ]] | ||
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+ | [[ 8. De novo assembly with Velvet ]] | ||
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+ | [[ 9. Using bwa for read mapping and SNP calling ]] | ||
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+ | [[ 9.1 Genome indexing for bra ]] | ||
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+ | [[ 9.2 Read mapping using bra ]] | ||
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+ | [[ 9.3 SNP calling using varscan ]] | ||
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+ | [[ 10. Useful references ]] |
Revision as of 19:15, 24 January 2016
6.1 Genome indexing for bowtie
6.2 Read mapping using topcoat
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