Quality Control and Preprocessing Talk - Revision history

Rf at 11:33, 10 May 2017

2017-05-10T11:33:48Z

2017-05-08T22:18:20Z

2017-05-08T22:02:20Z

2017-05-08T11:19:10Z

2017-05-08T11:18:38Z

2017-05-08T11:17:52Z

2017-05-08T11:17:08Z

2017-05-08T11:15:51Z

2017-05-08T11:14:55Z

2017-05-08T11:13:42Z

@@ Line 1: / Line 1: @@
 = Contents =
 * Data formats
@@ Line 15: / Line 13: @@
 * Text-based formats
 * If not compressed, it can be huge
-* Almost every programming language has a parser
+* Many bioinformatics packages have parsers for these (Parse: break up into more-easily handled components).
 [[File:fformat.png]]
-= Data formats =
+= Fastq format 1 =
-Fastq Format: Sequence quality encoding
 [[File:ascii.png]]
 = Sequence Data Format =
 Raw sequence data format (Flat/Binary files)
-* Fasta, Fastq, HDF5
+* Fasta, Fastq, HDF5 (this latter a new complex binary format).
 * Others: http://en.wikipedia.org/wiki/List_of_file_formats#Biology
-Processed sequence data format (Flat files)
+Processed (often into annotations) sequence data format (Flat files)
-* Column separated files containing genomic features
+* Column separated files containing genomic features and their chromosomal coordinates.
 * GFF and GTF
 * BED

@@ Line 114: / Line 114: @@
 [[File:pbsqg.png]]
 Good data = Consistent high quality along the read
 = Per base sequence quality, bad =
 [[File:pbsqb4.png]]
@@ Line 127: / Line 129: @@
 = Per tile sequence quality 1 =
 [[File:ptsq3.png]]
 = Per tile sequence quality 2 =
 [[File:ptsq4.png]]
@@ Line 159: / Line 163: @@
 * It is important to remove bad quality data as our confidence on downstream analysis will be improved.
 [[File:sf1.png]]
 = Sequence Filtering 2 =
 [[File:sf3.png]]

@@ Line 45: / Line 45: @@
 = GFF3 file example =
- ##gff-version 3
+[[File:gff.png]]
 = GFF graphicalGFF =
-representation
+* representation
-structure
+* structure
 [[File:sascha.png]]
@@ Line 170: / Line 124: @@
 Per sequence quality scores
-[[File:psqs.png]]
+[[File:bimods.png]]
 = Per tile sequence quality 1 =
-[[File:ptsq.png]]
+[[File:ptsq3.png]]
 = Per tile sequence quality 2 =
-[[File:ptsq2.png]]
+[[File:ptsq4.png]]
 = Per base sequence content =
-[[File:pbsc.png]]
+[[File:pbsc3.png]]
 = Per base GC content =
-[[File:pbgcc.png]]
+[[File:pbgcc3.png]]
 = Per sequence GC content =
-[[File:psgcc.png]]
+[[File:psgcc3.png]]
 = Per sequence N content =
-[[File:psnc.png]]
+[[File:psnc3.png]]
 = Sequence duplication levels =
-[[File:sdl.png]]
+[[File:sdl3.png]]
 = Overrepresented sequences and k-mer content =
-[[File:ovrep.png]]
+[[File:ovrep3.png]]
 = Sequence Filtering 1 =
 * It is important to remove bad quality data as our confidence on downstream analysis will be improved.
-[[File:sf.png]]
+[[File:sf1.png]]
 = Sequence Filtering 2 =
-[[File:sf2.png]]
+[[File:sf3.png]]
 = Sequence filtering tools =

@@ Line 171: / Line 171: @@
 [[File:psqs.png]]
-{|style="width:90%"
+{|style="width:80%"
 | Good data = most reads
 are high-quality sequences

@@ Line 171: / Line 171: @@
 [[File:psqs.png]]
-{|style="width:100%"
+{|style="width:90%"
 | Good data = most reads
 are high-quality sequences

@@ Line 172: / Line 172: @@
 [[File:psqs.png]]
 {|style="width:80%"
-! style="text-align:center;" | Good data = most reads are high-quality sequences
+! style="text-align:center;" | Good data = most reads
 are high-quality sequences
 | Bad data = Distribution
 with bi-modalities