Grabbag: Regular Expressions and Introduction to RNAseq
Materials
Regular expressions Resources
Bonus regular expressions exercises
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Use regular expressions to change the contents of the FASTA sequence file exampleGFP_raw.fasta to match the contents of the file exampleGFP_clean.fasta
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Use regular expressions to change the file contents of the file data1_raw.txt to match the contents of the file data1_clean.txt
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Generate a single masterful regular expression that can match a phone number in any of the following formats below and convert it to a phone number into this format: (XXX)-XXX-XXXX.
555-555-1234 555.555.4321 555 555 4321 (555).555.6789 (555)-555-0123
RNAseq Papers
- Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures
- How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
- Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays
- [Protocol paper] Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
- [Protocol paper] Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
RNAseq Resources
- What the FPKM? blogpost
- DESeq2 vs edgeR blog post
- DESeq2 Resources. These two resources are overly detailed but contain everything you ever wanted to know about DESeq2.