Protocols:HeliScopeCAGE read alignment: Difference between revisions
From FANTOM5_SSTAR
(Created page with "The data sequenced on Heliscope sequencers are post processed, in order to: *Discard the CAGE tags derived from the ribosomal DNA repeating unit, which is not contained in ...") |
No edit summary |
||
| Line 1: | Line 1: | ||
The data sequenced on Heliscope sequencers are post processed, in order to: | The data sequenced on Heliscope sequencers are post processed, in order to: | ||
*Discard the CAGE tags derived from the ribosomal DNA repeating unit, which is not contained in the genome assembly, by rRNAdust (developed by Timo Lassmann) | *Discard the CAGE tags derived from the ribosomal DNA repeating unit, which is not contained in the genome assembly, by rRNAdust (developed by Timo Lassmann). See [[Protocols:rRNAdust]] | ||
*Align the remained CAGE tags with the genome sequences with DELVE (developed by Timo Lassmann), which generate BAM files containing a single mapped position per read with mapping quality and alignments. | *Align the remained CAGE tags with the genome sequences with DELVE (developed by Timo Lassmann), which generate BAM files containing a single mapped position per read with mapping quality and alignments. | ||
*Retain only those reads with mapping quality corresponding to a 99% accuracy. | *Retain only those reads with mapping quality corresponding to a 99% accuracy. | ||
*Aggregate the 5'-end of those mapped CAGE tags as CAGE transcription starting site (CTSS) | *Aggregate the 5'-end of those mapped CAGE tags as CAGE transcription starting site (CTSS). | ||
Revision as of 14:40, 30 August 2012
The data sequenced on Heliscope sequencers are post processed, in order to:
- Discard the CAGE tags derived from the ribosomal DNA repeating unit, which is not contained in the genome assembly, by rRNAdust (developed by Timo Lassmann). See Protocols:rRNAdust
- Align the remained CAGE tags with the genome sequences with DELVE (developed by Timo Lassmann), which generate BAM files containing a single mapped position per read with mapping quality and alignments.
- Retain only those reads with mapping quality corresponding to a 99% accuracy.
- Aggregate the 5'-end of those mapped CAGE tags as CAGE transcription starting site (CTSS).
