Revision as of 09:09, 27 April 2012 by >RuiLiu
Hiseq_120313
Sample preparation
[1]
Flow cell
- s1-2: RL_B2_23s_Mar8.2012
- s5-6: RL_B3_24s_Mar8.2012
- s7-8: RL_Fib-Bulk_Mar8.2012
Mapping
Genome-miner: /media/SeqStore2/120315_HiSeq/Genome
Triton: /projects/zhang-lab/seqStore/120313_HiSeq/Genome
- prepare to submit jobs in triton
info file: File:B2 Indx73.info.txt
job file: File:B2 Indx73.job.txt
- An unique name for each library/index
- Excel or plain text for info/job files, tab-delimited plain text
- upload to triton (attn: space/line problems in nano format)
- tr "/r" "/n" < info.txt > info (convert to unix format)
- sed "s/73/xx/g" < 73.info > xx.info (convert to other index)
- qsub xx.job
- qstat | grep rul (check running status)
- qdel xxxx (kill job)
- triton contact info: Jim Hayes <jhayes@sdsc.edu> [2]
[3]
Validation
- multiple bands / unknown sequence in PCR results -> confirm primers on gDNA
- negative SNCs -> positive aliquot PCR
PCR-ID
|
Gene
|
Cat.
|
chr
|
pos
|
refBase
|
B2B3(GT)
|
Pf
|
Pr
|
PCR
|
'
|
SNC1 |
GLT25D2 (glycosyltransferase 25 domain containing 2) |
exon |
1 |
183907978 |
G |
G=7/T=3 |
CAGGGAGCCTTCATAGCTCA |
ACCTGAGTGACACGGAGACC |
189bp |
>chr1:183907885+183908073
|
|
|
|
|
|
|
|
|
|
|
|
QC good |
Fib |
P30 |
B2 |
B3 |
B2_MDA |
B3_MDA |
|
|
|
|
PCR |
1 band |
1 band |
|
|
|
|
|
|
|
|
seq. ID |
RL01_R |
RL02 |
RL03 |
RL04 |
RL05 |
RL06 |
|
|
|
|
seq. length |
350 |
160 |
160 |
160 |
160 |
70 |
|
|
|
|
blast |
183907925 183908073 |
183907925 183908071 |
183907932 183908074 |
183907932 183908074 |
183907930 183908071 |
183907997 183908070 |
|
|
|
|
identity |
100% |
100% |
100% |
100% |
100% |
100% |
|
|
|
|
SNC |
G |
G |
G |
G |
G (T? C?) |
N/A |
|
|
|
|
aliquot |
|
|
B2_Indx80,B2_Indx93,B3_Indx93 |
|
|
|
|
|
|
|
PCR-ID
|
Gene
|
Cat.
|
chr
|
pos
|
refBase
|
B2B3(GT)
|
Primers
|
PCR
|
SNC2 |
FLNB (actin binding protein 278) |
exon |
3 |
58104657 |
C |
C=6/G=3 |
TTTGGTACCCAAAGGTAAACTGA |
191
|
|
|
|
|
|
|
|
CAACCCATCTGCTCTCCATT |
>chr3:58104557+58104747
|
failed, repeat |
Fib |
P30 |
B2 |
B3 |
B2_MDA |
B3_MDA |
|
|
PCR |
|
|
|
|
|
|
|
|
seq. ID |
RL09 |
RL10_R |
RL11_R |
RL12 |
RL13 |
RL14 |
|
|
seq. length |
141 |
330 |
141 |
170 |
|
70 |
|
|
blast |
183907930 183908070 |
58104610 58104747 |
58104607 58104747 |
183907950 183908060 |
|
183907997 183908061 |
|
|
identity |
98% |
100% |
100% |
94% |
|
|
|
|
SNC |
SNC1? T? |
C |
C |
SNC1? T? |
no match |
SNC1? N/A |
|
|
aliquot |
|
|
|
|
|
|
B2_Indx80,B2_Indx82,B3_Indx92 |
|
PCR-ID
|
Gene
|
Cat.
|
chr
|
pos
|
refBase
|
B2B3(GT)
|
Primers
|
PCR
|
SNC3 |
PPP1R9A |
exon |
7 |
94918006 |
G |
A=3/G=6 |
AGTGTGCAGCAGGTTTCTCA |
223
|
|
|
|
|
|
|
|
CCTCTCAGATATGCAGAATGCTC |
>chr7:94917911+94918133
|
QC good |
Fib |
P30 |
B2 |
B3 |
B2_MDA |
B3_MDA |
|
|
PCR |
|
|
|
|
|
|
|
|
seq. ID |
RL17 |
RL18 |
RL19 |
RL20 |
RL21 |
RL22 |
|
|
seq. length |
184 |
270 |
846, chimeric |
1K, chimeric |
198 |
1K |
|
|
blast |
94917950 94918133 |
94917950 94918132 |
94917950 94918133 |
94917951 94918133 |
94917949 94918133 |
|
|
|
identity |
100% |
100% |
|
|
|
|
|
|
SNC |
G |
G |
G |
G |
G |
chr1 |
|
|
aliquot |
|
|
|
|
|
all B3 |
B3_Indx82,B3_Indx95,B3_Indx96 |
|