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置顶 · 薛良交-南京林业大学林学院

2019-11-6 20:06

http://linxue.njfu.edu.cn/sz/ShowJs.asp?id=358 http://linxue.njfu.edu.cn/info.php?cid=117 姓名： 薛良交 系别： 林木遗传育种系 职务： 教师 类别： 教授 最终学历： 博士研究生 最终学位： 理学博士 办公电话： 电子邮箱： lxue@njfu.edu.cn 教育经历： ...

个人分类: Bioinformatics|6872 次阅读|没有评论

Parsing of CIGAR and MD tag in SAM/BAM format

2015-1-1 01:05

Source code cigar http://cpansearch.perl.org/src/MNSMAR/GenOO-1.4.5/lib/GenOO/Data/File/SAM/Cigar.pm MDZ http://cpansearch.perl.org/src/MNSMAR/GenOO-1.4.5/lib/GenOO/Data/File/SAM/MDZ.pm Cigar and MDZ http://cpansearch.perl.org/src/MNSMAR/GenOO-1.4.5/lib/GenOO/Data/File ...

个人分类: Bioinformatics|5380 次阅读|没有评论

JC8: Young Genes out of the Male

2014-12-28 04:35

Young Genes out of the Male: an Insight from Evolutionary Age Analysis of the Pollen Transcriptome New paper on pollen transcriptome. http://www.cell.com/molecular-plant/abstract/S1674-2052(14)00043-4 Another paper published after the first one was submited for review. “ ...

个人分类: Journal Club|2466 次阅读|没有评论

向NCBI SRA提交数据

2014-11-15 05:17

0 Collect description information, prepare read files. Run md5sum (Linux) to get the md5 numbers of read files 1 Create BioProject Go to: http://www.ncbi.nlm.nih.gov/books/NBK47529/ Steps for SRA Submission-- Create a B ...

个人分类: Bioinformatics|10004 次阅读|没有评论

PSL format for blat software

2014-11-10 02:56

https://www.biostars.org/p/44633/ In general the coordinates in psl files are “zero based half open.” The first base in a sequence is numbered zero rather than one. When representing a range the end coordinate is not included in the range. Thus the first 100 bases of a sequence are represente ...

个人分类: Bioinformatics|3721 次阅读|没有评论

R code to split strings

2014-10-21 04:24

get_treat= function (x,in_split=\_,perl = T){ strsplit(x, in_split) ] } treat = as.character(sapply(samples_in ,get_treat))

个人分类: Bioinformatics|2341 次阅读|没有评论

Vcf.pm and tabix

2014-10-14 23:09

Yesterday, I wrote one code to load a vcf file with 20million lines into the memory. It's a huge hash, taking more than 5 G of memory. Today, I checked the perl module Vcf.pm. It's very fast and memory-efficency. Generally, I beleive their codes have been better tested than mine. I ...

个人分类: Bioinformatics|4815 次阅读|没有评论

Github

2014-10-10 23:28

网上很多code，自己懒得写就搜搜Github，Biostar http://davetang.org/muse/2011/01/28/perl-and-sam/

个人分类: Bioinformatics|2657 次阅读|没有评论

图书馆

2014-10-8 23:44

三更半夜，在网上查到一本书。基于以前的经验，自己买后，翻一个星期就懒得的翻了，所以就不想买。其实主要还是舍不得银子。 搜了一下，图书馆里也没有。于是就留了言推荐一下。一早起来，收到一封信说，已经给订了这本书。比秘书效率都高。表扬一下。（为什么比秘书效率高呢？因为我还没有秘书。）

个人分类: Live|2097 次阅读|没有评论

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