Jeff:LabNotes/Microbiome/2012-11-13
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Preliminary Sequencing Results
- Table below summarizes results
- The clonal rate is much better, averaging around 50% which is good
- The mapping rate is a little low for some of these. I will use Dr. Zhang's suggestion and using the quality trimming algorithm to see if it helps the mapping rate
- Some of the read numbers (unfiltered) are a little low. These will turn into good libraries if resequenced at a higher depth, and I will let Alan know which libraries to resequence
- Lane 7 failed due to an instrument error and will have to be resequenced
- I will focus more analysis on the Alzheimer's cortex library with enough reads
' | Sample | Type | Lane | Index | # Reads | Mapped (%) | % Clonal | # Usable Reads | ||
HL135 | 2041_059_Alzcbl_p | Neuron, alz_cerebellum | 5 | 34 | 7476700 | 2576033 (34.35) | 79.86 | 518850 | ||
HL135 | 2041_060_alzcbl_p | Neuron, alz_cerebellum | 5 | 37 | ||||||
HL135 | 60831_061_normal_p | Neuron, norm_ctx | 5 | 35 | 7522321 | 2325921 (30.92) | 51.25 | 1133796 | ||
HL135 | 60831_062_normal_p | Neuron, norm_ctx | 5 | 36 | 16340952 | 12017029 (73.54) | 61.66 | 4607752 | ||
HL135 | 60831_063_normal_p | Neuron, norm_ctx | 6 | 33 | 12367633 | 8354396 (67.55) | 56.66 | 3621045 | ||
HL135 | 60831_064_normal_p | Neuron, norm_ctx | 6 | 34 | 3870522 | 2470947 (63.84) | 40.74 | 1464367 | ||
HL135 | 60831_065_normal_p | Neuron, norm_ctx | 6 | 35 | 8175228 | 3443631 (42.12) | 33.42 | 2292841 | ||
HL135 | 60831_066_normal_p | Neuron, norm_ctx | 6 | 36 | 15497464 | 11475535 (74.05) | 60.76 | 4502562 | ||
HL135 | 60831_067_normal_p | Neuron, norm_ctx | 7 | 33 | ||||||
HL135 | 60831_068_normal_p | Neuron, norm_ctx | 7 | 34 | ||||||
HL135 | 2041_069_Alzcor_p | NeuN-, alz_cortex | 7 | 39 | ||||||
HL135 | 2041_070_Alzcbl_p | Neuron, alz_cerebellum | 7 | 32 | ||||||
HL135 | 2041_071_Alzcor_p | NeuN-, alz_cortex | 8 | 25 | 24439820 | 17625790 (72.12) | 52.85 | 8311147 | ||
HL135 | 2041_072_Alzcor_p | NeuN-, alz_cortex | 8 | 26 | 3553386 | 1878510 (52.87) | 48.07 | 975482 | ||
HL135 | 2041_073_Alzcor_p | NeuN-, alz_cortex | 8 | 29 | 7112256 | 3957668 (55.65) | 79.62 | 806608 | ||
HL135 | 2041_074_Alzcbl_p | Neuron, alz_cerebellum | 8 | 32 | 2499658 | 504487 (20.18) | 44.06 | 282209 |
2041_071_Alzcor_p| Analysis
- This library has enough reads for a proper analysis. Unfortunately, for the other 3 ALz cortex samples, each had its own issue (1 had high clonal, 1 had low mapping rate, and 1 had too few reads/can be resequenced).
- The overall plot shows a male (correct) with a lot of variation
- The APP and DYKR1A are on Chr21, so I will focus on that. APP is from 27,252,860 to 27,543,445 bp and DYKR1A is from 38,739,236 to 38,887,680.
- The Chr21 plot shows a few regions of high copy number.
- The middle region is ~100k downstream from the APP gene (contains CYYR1 gene), but it is on the same locus: 21q21.3. I don't know if this has any affect (would make more sense if it was upstream) or if the algorithm somehow shifted this region. I will need to get some opinions from other people
- I will need to sequence more Alz cortex libraries to get a better idea, and will begin to prepare more.