Difference between revisions of "Tips kang"
| Line 7: | Line 7: | ||
=TEXT(2.2323,"(0.00)")<br /> | =TEXT(2.2323,"(0.00)")<br /> | ||
(2.23)<br /><br /> | (2.23)<br /><br /> | ||
| + | |||
'''Softwares'''<br /> | '''Softwares'''<br /> | ||
''Deconseq'' <ref>[http://deconseq.sourceforge.net/ deconseq]</ref><br /> | ''Deconseq'' <ref>[http://deconseq.sourceforge.net/ deconseq]</ref><br /> | ||
| Line 12: | Line 13: | ||
63:/data/program/deconseq-standalone-0.4.3 <br /> | 63:/data/program/deconseq-standalone-0.4.3 <br /> | ||
/usr/bin/perl deconseq.pl -keep_tmp_files -f 800_both.fq -dbs bact,vir,arch -dbs_retain gmax <br /><br /> | /usr/bin/perl deconseq.pl -keep_tmp_files -f 800_both.fq -dbs bact,vir,arch -dbs_retain gmax <br /><br /> | ||
| + | ''ePCR''<br /> | ||
| + | Re-PCR<br /> | ||
| + | $ famap -tN -b genome.famap org/chr_*.fa<br /> | ||
| + | $ fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap<br /> | ||
| + | Work> /data/program/e-PCR-2.3.12/re-PCR -S genome.hash -n1 -g1 SSR.sts -o SSR.sts.mapped<br /> | ||
| + | SSR.sts<br /> | ||
| + | Mungbean_SSR_ID_1 CAAAAACATGAGTTGCACACAA TCATAACGCAGAACAGCGAA<br /> | ||
| + | Mungbean_SSR_ID_2 ATGTGTGTGAGCACCTCGAC TTTGGCCATGCAAGATGTAA<br /> | ||
| + | Mungbean_SSR_ID_4 GCGGTTCACCTAGCCATAAA GGACCCTTCTGTGCGTGTAT<br /> | ||
| + | Mungbean_SSR_ID_5 GTTTGTGCTGCGGATTCTTT TTGGCAATTTGGACTAAGGC<br /> | ||
| + | Mungbean_SSR_ID_7 TTGACCCAAAACTTACCAATTT GCTAAGGACTGGGGGTCTTC<br /> | ||
| + | <br /> | ||
'''추천 논문'''<br /> | '''추천 논문'''<br /> | ||
Paterson, A.H., M. Freeling, H. Tang and X. Wang. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372. <ref>[http://www.annualreviews.org/doi/abs/10.1146/annurev-arplant-042809-112235 Paterson, A.H., M. Freeling, H. Tang and X. Wang. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372. ]</ref><br /> | Paterson, A.H., M. Freeling, H. Tang and X. Wang. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372. <ref>[http://www.annualreviews.org/doi/abs/10.1146/annurev-arplant-042809-112235 Paterson, A.H., M. Freeling, H. Tang and X. Wang. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372. ]</ref><br /> | ||
<references /> | <references /> | ||
Revision as of 06:02, 17 March 2014
Python
Fisher's exact test
from scipy import stats
oddsratio, pvalue = stats.fisher_exact([[A,B], [C, D]]) [1]
Excel
=TEXT(2.2323,"(0.00)")
(2.23)
Softwares
Deconseq [2]
Illumina read의 contamination을 확인한다.
63:/data/program/deconseq-standalone-0.4.3
/usr/bin/perl deconseq.pl -keep_tmp_files -f 800_both.fq -dbs bact,vir,arch -dbs_retain gmax
ePCR
Re-PCR
$ famap -tN -b genome.famap org/chr_*.fa
$ fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
Work> /data/program/e-PCR-2.3.12/re-PCR -S genome.hash -n1 -g1 SSR.sts -o SSR.sts.mapped
SSR.sts
Mungbean_SSR_ID_1 CAAAAACATGAGTTGCACACAA TCATAACGCAGAACAGCGAA
Mungbean_SSR_ID_2 ATGTGTGTGAGCACCTCGAC TTTGGCCATGCAAGATGTAA
Mungbean_SSR_ID_4 GCGGTTCACCTAGCCATAAA GGACCCTTCTGTGCGTGTAT
Mungbean_SSR_ID_5 GTTTGTGCTGCGGATTCTTT TTGGCAATTTGGACTAAGGC
Mungbean_SSR_ID_7 TTGACCCAAAACTTACCAATTT GCTAAGGACTGGGGGTCTTC
추천 논문
Paterson, A.H., M. Freeling, H. Tang and X. Wang. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372. [3]
