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Showing posts from December, 2016

R bookdown: Error: ! LaTeX Error: Environment rmdtip undefined. Error: Failed to compile bookdown-demo.tex.

! LaTeX Error: Environment rmdtip undefined. Error: Failed to compile bookdown-demo.tex. See bookdown-demo.log for more info. How to solve? User https://raw.githubusercontent.com/rstudio/bookdown/master/inst/examples/latex/preamble.tex to replace your file.

How to understand the TruSeq Stranded mRNA?

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How is strandedness maintained after DNA amplification? Strandedness is maintained via the directionality of the adapters. The p7 adapter will be on the 3' end of the cDNA strand. As a consequence, the cDNA strand is sequenced. Second strand synthesis is performed using dUTP in place of dUTP and a high fidelity polymerase that cannot process through dUTP template is used for PCR enrichment. As a result, only the first strand product is amplified and the strand information is retained based on the p5 and p7 adapter orientation. The P5 end is sequenced first, then the P7; another name for the P5 is the "Universal adapter" (UNad) and P7 is "Index-containing adapter" (IndexAd), because it has the index for de-multiplexing multiple libraries run on the same lane. For example, the strand of the gene is "+", read1 should be mapped to the reverse strand of the reference genome. http://nextgen.mgh.harvard.edu/IlluminaChemistry.html h

Bookdown: error: Failed to compile bookdown-demo.tex.

Error: Message: Error: Failed to compile bookdown-demo.tex. Warning messages: 1: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-demo.tex"' had status 127 2: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-demo.tex"' had status 127 3: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-demo.tex"' had status 127 Reasons: This is because I didn't install XeLaTeX How to solve: * Install XeLaTeX on Windows Weblink: http://www.texts.io/support/0002/ * Restart the Rstudio

python4bioinfor: pass by reference for dictionary

Arguments are  passed by assignment . The rationale behind this is twofold: the parameter passed in is actually a  reference  to an object (but the reference is passed by value) some data types are mutable, but others aren't So: If you pass a  mutable  object into a method, the method gets a reference to that same object and you can mutate it to your heart's delight, but if you rebind the reference in the method, the outer scope will know nothing about it, and after you're done, the outer reference will still point at the original object. If you pass an  immutable  object to a method, you still can't rebind the outer reference, and you can't even mutate the object. To make it even more clear, let's have some examples. List - a mutable type Let's try to modify the list that was passed to a method: def try_to_change_list_contents ( the_list ): print 'got' , the_list the_list . append ( 'four' ) print '

How to understand SAM flag

# Binary Decimal Hexadecimal Description 1 1 1 0x1 Read paired 2 10 2 0x2 Read mapped in proper pair 3 100 4 0x4 Read unmapped 4 1000 8 0x8 Mate unmapped 5 10000 16 0x10 Read reverse strand 6 100000 32 0x20 Mate reverse strand 7 1000000 64 0x40 First in pair 8 10000000 128 0x80 Second in pair 9 100000000 256 0x100 Not primary alignment 10 1000000000 512 0x200 Read fails platform/vendor quality checks 11 10000000000 1024 0x400 Read is PCR or optical duplicate 12 100000000000 2048 0x800 Supplementary alignment Instruction : enter whatever SAM flag (e.g. 99) to get a quick interpretation of its meaning, or click on arbitrary rows to select/deselect them to calculate the corresponding flag value. As you can see, your typed flag is a just sum of the matched bits in green. http://www.samformat.info/sam-format-flag

转载:青千注意事项

(上次洋洋洒洒写了一页,写完了点发送键,竟然被告知得重新登陆,万恶的mitbbs. com竟然将刚刚输入的文字全盘清空了。以下是缩写版,仅供参考) 准备材料:推荐信抬头可以写Youth 1000 Talent Program。所发文章中通讯作者最重 要,其次是第一。引用数多的更重要。然后是高分文章(如果国内没有相关的小同行了 解情况的话,说明一下杂志在本领域内的地位有帮助)。列举的材料都要准备证明材料 。引用按SCI数据库为标准,其它的最好加证明材料。数字要准确,不要在小问题上被 抓辫子。 评审:委员有院士,千人和青千,杰青长江和一些做得很好的业内同行。评审应该是很 公平的。 答辩:一开始几批都没有设限,评审过了都可以上。后来好像就有了淘汰率。答辩和国 外的报告有很大差别。首先得严格按给的框框来准备:个人简介、成果、未来计划、平 台。个人简介要快,成果要讲的通俗易懂,最好列出发的文章,指出成果重要性,你所 发挥的作用,引用情况。高分文章如果每年引用才1~5篇会有很强的负面效果。背景是 生物类发的所谓高分文章现在压得学术界喘不过气来。实际上CNS的文章也并不比各领 域top期刊文章好。如果CNS每年引用上不去就正好成了靶子。建议不要着重突出。独立 PI的基金一定要列出,基金号要给出。系统性的工作很重要。有些评委会问你以前不做 这个怎么突然改方向了。计划和平台一定要留好时间3张幻灯片也够了,但要让评委看 到你去的地方确实能让你发挥作用。 换单位:评委会问。影响不得而知。拿到后实际换的时候主要是原单位要答应放人。反 正很曲折。有许多学校老早就让你从他们那报,说是拿到后不满意还可以走。不是那么 容易。申请青千时的合同99.9%都是意向性的为应付青千的东西。事先要确认真正合同 要另外再签。能让他们写上具体配套的条件最好,到时也可以作为谈判的一个砝码。国 内答应的东西有很多水分。 总体趋势是看好和重点投资青千的。主要是大千人放的太多,80%以上全职千人3个月都 不到。祝大家申请成功。 References: http://www.mitbbs.com/article_t/Returnee/13500299.html

Nice Epigenetic related Blogs

Epigenetic Blogs From Zymo http://www.zymoresearch.com/epigenetics-blog/epibeat