...
| Code Block |
|---|
cds cp -r $BI/ngs_course/listeria_RNA_seq/data listeria_RNA_seq |
If you want to skip the read alignment step...
To get right to the new stuff you can copy the mapped read BAM files and the reference sequence files that you will need from here:
| Code Block |
|---|
cds
cp -r $BI/ngs_course/listeria_RNA_seq/mapped_data listeria_RNA_seq
|
Then skip the mapping steps below.
File Name | Description | Sample |
|---|---|---|
| Single-end Illumina 36-bp reads | wild-type, biological replicate 1 |
| Single-end Illumina 36-bp reads | ΔsigB mutant, biological replicate 1 |
| Single-end Illumina 36-bp reads | wild-type, biological replicate 2 |
| Single-end Illumina 36-bp reads | ΔsigB mutant, biological replicate 2 |
| Reference Genome sequence (FASTA) | Listeria monocytogenes strain 10403S |
| Reference Genome features (GFF) | Listeria monocytogenes strain 10403S |
...
- Oliver, H.F., et al. (2009) Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 10:641. Pubmed
You can view the data in the ENA SRA here: http://www.ebi.ac.uk/ena/data/view/SRP001753the ENA SRA here: http://www.ebi.ac.uk/ena/data/view/SRP001753
If you want to skip the read alignment step...
To get right to the new stuff, you can copy the mapped read BAM files and the reference sequence files that you will need from here:
| Code Block |
|---|
cds
cp -r $BI/ngs_course/listeria_RNA_seq/mapped_data listeria_RNA_seq
|
Then, skip the mapping and SAM/BAM conversion, sorting, indexing steps below.
Installing Bioconductor modules for R
...