Analyzing RNA-Seq data for differential gene expression
We will .
Download data files
File Name | Description | Sample |
|---|---|---|
| Single-end Illumina 36-bp reads | wild-type, replicate 1 |
| Single-end Illumina 36-bp reads | δsigB mutant, replicate 1 |
| Single-end Illumina 36-bp reads | wild-type, replicate 2 |
| Single-end Illumina 36-bp reads | δsigB mutant, replicate 2 |
| Reference Genome | Listeria monocytogenes strain 10403S |
http://www.ebi.ac.uk/ena/data/view/SRP001753
http://www.biomedcentral.com/1471-2164/10/641
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
- Data files
- RNA-Seq data in FASTQ format (Ex: dataset1.fastq, dataset2.fastq)
- Genome sequence files
- Genome sequence in FASTA format (Ex: REL606.fna)
- Genome sequence gene annotations in GFF3 format (Ex: REL606.gff3)
Install software
FAR - the Flexible Adaptor Remover
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Bowtie2 (first choice)
| Code Block |
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module load bowtie |
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