Bioinformatics: Featurecount Install and more

Subhead-2.0.2

https://github.com/ShiLab-Bioinformatics/subread/releases

  1. wget https://github.com/ShiLab-Bioinformatics/subread/releases/download/2.0.2/subread-2.0.2-macOS-x86_64.tar.gz
  2. tar -xvf subread-2.0.2-macOS-x86_64.tar.gz
  3. mv -v subread-2.0.2-macOS-x86_64 apps/
  4. nano .zshrc
  5. add: Export PATH=$PATH:/Users/__/___/subread/bin
  6. get gif or make gif: https://useast.ensembl.org/Mus_musculus/Info/Index
  7. use eg) featureCounts -T 5 -a annotation-subread/mouse_ensembl/Mus_musculus.GRCm38.102.gtf  -o quants/KO_count_matrix.txt HISAT2/SRR2936859.bam HISAT2/SRR2936860.bam HISAT2/SRR2936861.bam HISAT2/SRR2936864.bam HISAT2/SRR2936865.bam
  8. Cat file | less
  9. Cat file | cut f1,7-10> new file (could rename of column in excel!!!)

reference:

https://rdrr.io/bioc/Rsubread/man/buildindex.html

https://github.com/ShiLab-Bioinformatics/subread/releases

HISAT2 Install and more

  1. Download -version HISAST2 2.2.1 OSX_X86_64 : https://daehwankimlab.github.io/hisat2/download/#version-hisat2-221
  2. Put everything proper location: eg) /Users/___/___/hisat2-2.2.1
  3. Add Path into .zshrc: export PATH=$PATH:/Users/___/___/hisast2-2.2.1
  4. Download reference seq: eg) wget  https://genome-idx.s3.amazonaws.com/hisat/mm10_genome.tar.gz
  5. Need unzip: eg) tar -xvf mm10_genome.tar.gz
  6. Run alignment: eg) hisat2 -q –rna-strandness R -x hISAT2/mm10/genome -U data/SRR2936865_trimmed.fastq.gz | samtools sort -o HISAT2/SRR2936865.bam

If you need some more help:

Installation:

40. 이해 / understanding

다른 사람을 이해할 수 없을 땐

다른 사람이 된 것처럼 생각해 봐요

그래도 완전히 그 사람을

그 사람의 상황을 안다고 여기지 마세요

내 자신에 대해서도 완전히 파악하는 것은 힘든 일이어요

When you can’t understand another

Pretend you’re someone else

Still don’t assume you know his/her situation and him/her completely

It’s even hard for you to fully understand yourself

It’s even hard for me to fully understand myself

죽음/ Death

죽음은 많은 걸 포함한다.

죽음은 한 사람의 삶과 살아온 역사를 품는다.

죽음은 신화와, 종교와, 철학과 과학도 품는다.

죽음은누군가가가벼이넘기려한다해도결국경건하고경이롭다.

Death embraces many things:

A person’s life and history,

mythology, religion, philosophy and science.

Death is ultimately godly, honoring, glorious and wonder even if some try to take it lightly.

Embolism vs Thrombus

An embolus is any foreign materials that move with blood flow. The material of an embolus may be: air, fat, blood clot and any others.

A thrombus is a blood clot.

Both can block blood flow and increase the risk of a hear attack, pulmonary embolism and/or stroke

Think!! (Q1) Why do blood clots form inside the vessels, and why do blood clots increase with aging?

Think!! (A1) When we have scars outside, a blood clot forms to protect and stop bleeding. If blood vessels have internal wounds, blood clots form as well to protect inside organs and vessels . After the wounds have healed, the blood clots are detached like outside scars, and blood clots move away as thrombus, and could block the vessels.

Think (Q2) Could we resolve formed blood clot scrubs inside blood vessels safely and slowly or increase attachment (never dropping forever)? Instead of inhibiting formation process of the blood clots which could be dangerous, causing non-stop bleeding.

Design a site like this with WordPress.com
Get started