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--- archive:bioinformatic_tools:bwa [2011/05/23 02:25]
svohr [After SeqPrep]
+++ archive:bioinformatic_tools:bwa [2011/05/30 19:30]
svohr
@@ Line 29: / Line 29: @@
 </code>
+Note that BWA does seem to accept gzipped files, so there is no need to ungzip the read files, though the documentation doesn't mention this.
 ===== Quirks =====
 The SAM formatted alignments include a column labeled "inferred insert length" by the BWA manual, but in the SAM specification it is described as the "template length" or distance between the leftmost mapped base to the rightmost mapped base. The second description seems to
@@ Line 87: / Line 88: @@
 {{:bioinformatic_tools:run2_bc08_seqprep_histogram_r2.png|}}
+===== After Quake =====
+This process was repeat on the data after Quake correction. In addition to the paired reads and merge reads, Quake separates the reads whose pair could not be successfully corrected.
+{{:bioinformatic_tools:run1_quake_histogram.png|}}
+{{:bioinformatic_tools:run2_bc07_quake_histogram.png|}}
+{{:bioinformatic_tools:run2_bc08_quake_histogram.png|}}
+==== Mean Lengths ====
+Run 1
+| Template | 151.7 |
+| Merged   | 113.3 |
+| Single   | 65.7  |
+Run 2 bc07
+| Template | 250.3 |
+| Merged   | 142.5 |
+| Single   |  88.8 |
+Run 2 bc08
+| Template |  94.5 |
+| Merged   | 104.2 |
+| Single   |  61.3 |

Banana Slug Genomics