Jeff:LabNotes/Microbiome/2012-11-13

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Revision as of 01:23, 14 November 2012 by >Jgole (Created page with " =='''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 lo...")
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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.

File:11-13-12 allchr.jpeg File:11-13-12 21chr.jpeg