Table 3. Summary of Illumina base calling and alignments.
|
Genotype |
WT |
WT |
WT |
Nrl−/− |
Nrl−/− |
Nrl−/− |
|---|---|---|---|---|---|---|
| Sample 1 | Sample 2 | Sample 3 | Sample 1 | Sample 2 | Sample 3 | |
| Total reads |
35,872,080 |
41,785,800 |
49,076,400 |
46,689,240 |
48,480,240 |
48,656,040 |
| PF Reads |
29,603,280 |
33,251,160 |
37,642,800 |
36,472,800 |
37,119,960 |
36,823,320 |
| |
82.7% |
79.7% |
76.9% |
78.2% |
76.7% |
75.8% |
| BWA alignments |
24,992,271 |
27,922,997 |
32,085,799 |
30,960,565 |
31,374,578 |
31,257,335 |
| TopHat alignments | 30,769,939 | 34,177,120 | 39,222,596 | 38,289,469 | 38,744,790 | 38,593,533 |
Each of the 3 week old WT and Nrl−/− retina sample was sequenced on a separate lane of the Illumina GAIIx flow cell to obtain 35 to 49 million raw reads. Over 75% of the raw reads passed Illumina’s read chastity threshold to yield 29 to 37 million usable PF reads. TopHat mapping always gave significantly more alignments than BWA because of its ability to map across the splice junctions. A relatively smaller numbers of reads and alignments for WT samples 1 and 2 are not a matter of concern as FPKM normalization was used to assess the transcript isoform expression. WT=wild type. PF=pass filter