Quality of Mapping Talk - Revision history

Rf at 12:22, 9 May 2017

2017-05-09T12:22:14Z

Rf at 12:20, 9 May 2017

2017-05-09T12:20:52Z

Rf at 12:20, 9 May 2017

2017-05-09T12:20:14Z

Rf: Created page with "= Mapping quality control = Some issues are only detectable in the context of the genome: * Duplicate reads * Fragment size distribution * Gene coverage * Completeness of data..."

2017-05-09T12:15:35Z

Created page with "= Mapping quality control = Some issues are only detectable in the context of the genome: * Duplicate reads * Fragment size distribution * Gene coverage * Completeness of data..."

New page

= Mapping quality control =
Some issues are only detectable in the context of the genome:
* Duplicate reads
* Fragment size distribution
* Gene coverage
* Completeness of data

= Duplicate reads =

[[File:dups.png]]

* Only detectable with paired end reads

= Duplicate reads 2 =
* Duplicates can be PCR artefacts
* Duplicates can be real, from highly expressed transcripts
* For RNA-seq, removing duplicates is still being debated
* We don’t remove them, but it’s important to:
:- assess the duplicate rate
:- determine whether the duplicate rate can be explained by a few highly expressed genes

= Fragment size distribution =

{|
| * Should correspond with
fragment size selected
during library preparation
* Take into account that
reads can span introns
when calculating fragment
size
|-
| [[File:inssz.png]]
|}

= Gene coverage =

{|
| * Read coverage of the gene
should be uniform
* Less coverage at the ends
is expected because of
degradation of the RNA
* There should be no 5' nor
3' bias
|-
| [[File:gcov.png]]
|}

= Completeness of data =

{|
| * From a saturated RNASeq dataset,
all known splice junctions should be
rediscovered.
* Check saturation by resampling
resampling 5%,10%,..,100% of
alignments, detect splice junctions
from each subset and compare them to
reference gene models
|-
| [[File:comp.png]]
|}

@@ Line 50: / Line 50: @@
 = Completeness of data =
-{|
+* From a saturated RNASeq dataset, all known splice junctions should be rediscovered.
-| * From a saturated RNASeq dataset,
+* Check saturation by resampling resampling 5%,10%,..,100% of alignments, detect splice junctions from each subset and compare them to reference gene models
 all known splice junctions should be
-rediscovered.
+[[File:comp.png]]