Personal tools

Protocols:rRNAdust: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "This step is required to remove reads corresponding to rRNA from Helicos CAGE datasets. Since the error rate of Helicos is high and includes many insertion / deletion errors...")
 
No edit summary
 
Line 4: Line 4:


All reads matching the reference rRNA sequences with up to 2 errors are discarded at this step.
All reads matching the reference rRNA sequences with up to 2 errors are discarded at this step.
Software available at fantom.gsc.riken.jp/5/suppl/rRNAdust/

Latest revision as of 11:11, 19 February 2015

This step is required to remove reads corresponding to rRNA from Helicos CAGE datasets.

Since the error rate of Helicos is high and includes many insertion / deletion errors, the only viable option was to match sequences against rRNA sequences (U13369.1) using a non-heuristic alignment algorithm. Due to the amount of data a SSE parallelized version of Myers bit-parallel algorithm was implemented.

All reads matching the reference rRNA sequences with up to 2 errors are discarded at this step. Software available at fantom.gsc.riken.jp/5/suppl/rRNAdust/