Sail through Sapelo2

If you are a first-time user, you can read through this guide from the beginning. However, if you already have your own workflow, you might want to jump to the tips section to check if there are some more little things you can do to make your workflow more efficient. SSH client: handy tool makes a handyman First thing first, choose a suitable SSH client. Of course, you can use terminal/power-shell to ssh into the cluster, but some GUI might make things easier....

October 18, 2021 · 6 min · Chen Hsieh

Using AlphaFold at UGA

At UGA you can run AlphaFold on two platforms, GACRC and COLAB. The code on GACRC might be closer to the original one released by Deepmind. The COLAB one made the ‘sequence alignment’ step quicker with potentially reduced accuracy. The good news is that the results from both of them look the same to my eyes. After getting the results, just use software like PyMol to open the .pdb file to visualize the 3D model....

October 9, 2021 · 2 min · Chen Hsieh

my leetcode journey

My frustration and ugly codes Being a bioinformatic student, I have no problem using other people’s software and plug in required data. I can also interpret data correctly for most of the cases. However, I am always nervous about not having a really solid training in quantitative skills. This is making me replaceble. It is easy to teach a software engineer biology knowledge but it is far more harder to...

July 1, 2021 · 9 min · Chen Hsieh
from Aeon Flux

[PhD Journey] 2021 Q1

PhD 是一趟主動學習的旅程,對我來說除了獲取知識以外,情勢視讀與決策能力更是我希望能成長的方向,過程中的每件小事細品都有啟示 January:在前...

April 1, 2021 · 5 min · Chen Hsieh

How I get an idea of a new research topic

It’s really easy to get side-projects as a bioinformatic student. Although it is exciting to have a side-project to work on for the possibility of co-authorship or any possible reward, it is more important to be reallistic on the time commitment. Increasing the efficiency of the learning process is the topic I am currently focusing on. Especially when dabbling into a new realm of research topic, I always ended up with a lot of browser tabs without really getting the idea....

March 7, 2021 · 4 min · Chen Hsieh

2021 新展望: Seeking of Best Practice

I have been feeling I rely on luck for a long time. I do not have a real established routine. I am abusing little tricks to have little win. Even the little wins are not real wins, they are just acceptable result to be honest. ...

January 3, 2021 · 2 min · Chen Hsieh

RNA-Sick@Day14 > 檢定只是裝飾而已,上面的大人物是不會懂的|篩選表現量有顯著差異的基因 feat. edgeR

原文發表於第 11 屆 iT 邦幫忙鐵人賽 (https://ithelp.ithome.com.tw/articles/10222248) 超級比一比之 CPM, FPKM, TPM RNA-Seq 的主要目的之一就是找到試驗設計處理組間的差異表現基因 (Differential Expression Genes, DEG),這些基因之所以差異表...

September 29, 2019 · 5 min · Chen Hsieh

RNA-Sick@Day13 > 萬物皆虛,萬事皆允|不用 alignment 推估表現量 feat. kallisto

原文發表於第 11 屆 iT 邦幫忙鐵人賽 (https://ithelp.ithome.com.tw/articles/10222244) 放棄比對的話,新世界的大門就開啟囉 想知道手邊的兩條序列有多像,最直觀的方式就是把他們排在一起比一比。但是排列...

September 28, 2019 · 4 min · Chen Hsieh

RNA-Sick@Day12 > 路遙知馬力,日久見人心|用燕尾服套裝將序列比對到參考對象上 feat. Bowtie2

原文發表於第 11 屆 iT 邦幫忙鐵人賽 (https://ithelp.ithome.com.tw/articles/10221594) 燕尾服套裝軟體取名的惡趣味總讓我想到黑暗大法師 RNA-Seq 主要目的之一就是推估樣本中轉錄產物豐富度,這個過程可以分成 短...

September 27, 2019 · 4 min · Chen Hsieh

RNA-Sick@Day11 > 轉錄體補完計畫|比對線上資料庫註解序列 feat. Trinotate

原文發表於第 11 屆 iT 邦幫忙鐵人賽 (https://ithelp.ithome.com.tw/articles/10221160) 代號之卷 (Component, Gene, Isoform) 新組裝轉錄體後,會產出一個 Trinity.fasta 的序列檔案,其中包含所有可能的轉錄產物 isoform,以下是針對序...

September 26, 2019 · 2 min · Chen Hsieh

RNA-Sick@Day10 > 我來組成頭部|把短片段序列組裝成轉錄體 feat. Trinity

原文發表於第 11 屆 iT 邦幫忙鐵人賽 (https://ithelp.ithome.com.tw/articles/10220238) 神奇的轉錄體拼圖 透過 RNA-Seq 進行轉錄體分析,比起使用微陣列晶片 (microarray) 偵測起基因表現量/轉錄產物量 (transcript level),除了背...

September 25, 2019 · 3 min · Chen Hsieh

RNA-Sick@Day9 > 斷開序列,斷開一切的牽連|把品質不佳的序列剔除掉 feat. Trimmomatic

原文發表於第 11 屆 iT 邦幫忙鐵人賽 (https://ithelp.ithome.com.tw/articles/10219913) 自動修剪機,修鹼基 fastq 檔案中存放的資料包括序列及其對應的品質,雙端定序的結果分別存放在結尾標記 -1 和 -2 的檔案中。...

September 24, 2019 · 2 min · Chen Hsieh

RNA-Sick@Day8 > Raw Data 是什麼,能吃嗎?| 一鍵了解序列品質 feat. FastQC

原文發表於第 11 屆 iT 邦幫忙鐵人賽 (https://ithelp.ithome.com.tw/articles/10219591) 進入轉錄體流程篇 已經寫完了奠定基礎功的七篇,第八天開始就會是基礎分析流程之工具使用。想當初我剛開始進行碩論中...

September 23, 2019 · 3 min · Chen Hsieh