SEQ03 - recreation in 12-2018

2018-11-29 Thursday

I’m re-creating these sample files in order to get a clean copy of L0410, which is corrupted.

2018-10-05 Friday

Moving lines from this notebook to All samples filtering

2018-10-04 Thursday

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

2018-10-03 Wednesday

started trim, map, and call SNPs
need to cat total raw snps into master file

2018-09-24 Monday

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

2018-09-13 Thursday

pooled 3 baits into seq Ron

baits 1
baits 2
baits 3
baits.nb.html
baits.pdf
Indexes in this seq are 1-12

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

seq_prep.nb.html

C4E67CE8-BA70-4CB1-90CC-2087D0CEDD2A.pdf

seq_processing.html seq_processing.ipynb

index-seq18.tsv

P073_process.sh

P074_process.sh

P075_process.sh

P076_process.sh

P077_process.sh

P078_process.sh

P083_process.sh

P084_process.sh

P085_process.sh

P086_process.sh

P087_process.sh

P088_process.sh rename_28.nb.html

rename_28.sh SEQ18_all_rename.sh

SEQ18_cat_all.sh

SEQ18_move_radlogs.sh

SEQ18_process_all.sh

seq_proc.nb.html