-
Recent Posts
Recent Comments
- Davo on DESeq vs. edgeR vs. baySeq
- Alex Williams on DESeq vs. edgeR vs. baySeq
- Davo on Perl and SAM
- Peter Briggs on Perl and SAM
- dongyu on DESeq vs. edgeR vs. baySeq
Tag Cloud
6mer annotation bidirectional genes bioinformatics CAGE clustering coexpression correlation cryptography de novo assembly DGE etc fork genome GO graph heatmap histones home mapping miRNA motif neurobiology parser pathway pca perl promoter python R refseq rnaseq SAM scan spearman statistics trna ubuntu visualisationArchives
Meta
Tag Archives: CAGE
Clustering mapped reads
When working with reads that represent transcriptional starting sites (TSSs), such as CAGE data, reads do not always map at the same position. This is mainly because RNA Polymerase II initiates transcription from different positions. One way to study the … Continue reading
Visualising FANTOM3 human CAGE data
First download the relevant tables from here. Download tss_library_expr_summary.tsv.bz2, tss_summary.tsv.bz2 and rna_lib_summary.tsv.bz2 and bunzip2 the files. According to information derived from rna_lib_summary.tsv there are 13,897 CAGE tags from the prostate gland (rna_lib_id = HBA). Double check this: Genomic coordinates of … Continue reading