- cat raw snps to all_raw_snps.vcf
- upload notebook to the APCL_analysis directory and deleted from here to avoid version errors.
- tried to merge the files, ran into some problems that are preserved in the notebook. This note helped: 2016-11-23 Wednesday
- ended the day waiting for the vcf-merge to finish. The output file was slowly increasing in size but I’m not sure if it is full of nonsense columns
- started trim, map, and call SNPs
- need to cat total raw snps into master file
- Started working on seq28
- there were some problems with barcode_splitter.py but it turned out my local drive was trying to use a different version of python.
- Added python2 to the bash at the top to fix.
SEQ18 = SEQ28
- pooled 3 baits into seq Ron
- Cleaned and quantified
- Diluted to 10nM - 13.2 seq + 17.8 pH2O
- Sent for sequencing
- Bioanalyzer of seq came back that it was only 0.88nM - check the math in the seq_prep file. - recalculating shows SEQ28 is 7.5nM. I unintentionally diluted that to send to sequencer.
- Added columns to the database - this notebook is different because we added lines to the code to adjust the number of columns in the database and rename columns. Future seqs don’t need these lines of code.
Samples that came back with fewer than 100,000 reads:
1 | L3172 |
2 | L3173 |
3 | L3174 |
4 | L3175 |
5 | L3177 |
6 | L3186 |
7 | L3195 |
8 | L3197 |
9 | L3198 |
10 | L3204 |
11 | L3206 |
12 | L3218 |
13 | L3220 |
14 | L3229 |
15 | L3246 |
16 | L3247 |
17 | L3263 |
18 | L5505 |
19 | L5506 |
20 | L5508 |
21 | L5516 |
22 | L5517 |
23 | L5518 |
24 | L5519 |
25 | L5522 |
26 | L5523 |
27 | L5524 |
28 | L5525 |
29 | L5526 |
30 | L5527 |
31 | L5540 |
32 | L5541 |
33 | L5544 |
34 | L5545 |
35 | L5559 |
36 | L5572 |
37 | L5573 |
38 | L5616 |
39 | L5617 |
40 | L5619 |
41 | L5624 |
42 | L5625 |
43 | L5626 |
44 | L5627 |
45 | L5628 |
46 | L5629 |
47 | L5630 |
48 | L5631 |
49 | L5632 |
50 | L5633 |
51 | L5634 |
52 | L5603 |
53 | L5613 |
54 | L5645 |
55 | L5646 |
56 | L5647 |
57 | L5648 |
58 | L5649 |
59 | L5650 |
60 | L5651 |
61 | L5652 |
62 | L5653 |
63 | L3666 |
64 | L3667 |
65 | L3669 |
66 | L3671 |
67 | L3672 |
68 | L3675 |
69 | L3677 |
70 | L3680 |
71 | L3682 |
72 | L3683 |
73 | L3684 |
74 | L3685 |
75 | L3687 |
76 | L3694 |
77 | L3698 |
78 | L3718 |
79 | L3740 |
80 | L3304 |
81 | L3306 |
82 | L3314 |
83 | L3322 |
84 | L3329 |
85 | L3350 |
86 | L4478 |
87 | L4479 |
88 | L4487 |
89 | L4498 |
90 | L4499 |