Difference between revisions of "Tips kang"
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from scipy import stats<br /> | from scipy import stats<br /> | ||
oddsratio, pvalue = stats.fisher_exact([[A,B], [C, D]]) <ref name="fishers exact">[http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html scipy, fisher's exact] </ref><br /> | oddsratio, pvalue = stats.fisher_exact([[A,B], [C, D]]) <ref name="fishers exact">[http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html scipy, fisher's exact] </ref><br /> | ||
| − | <br /> | + | 63:/home/k821209/py/NGS/vcfq2fa.py : vcfutil로 만들어진 fq 파일을 fa로 변환<br /><br /> |
'''Excel'''<br /> | '''Excel'''<br /> | ||
=TEXT(2.2323,"(0.00)")<br /> | =TEXT(2.2323,"(0.00)")<br /> | ||
Revision as of 05:52, 21 March 2014
Python
Fisher's exact test
from scipy import stats
oddsratio, pvalue = stats.fisher_exact([[A,B], [C, D]]) [1]
63:/home/k821209/py/NGS/vcfq2fa.py : vcfutil로 만들어진 fq 파일을 fa로 변환
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
Mummer, alignment draft genome to finished genome
$nucmer --prefix=ref_qry ref.fasta qry.fasta
$show-coords -rcl ref_qry.delta > ref_qry.coords
$show-aligns ref_qry.delta refname qryname > ref_qry.aligns
$show-tiling ref_qry.delta > ref_qry.tiling
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]
