User: Hughie

gravatar for Hughie
Hughie30
Reputation:
30
Status:
New User
Location:
guangzhou
Last seen:
6 days, 13 hours ago
Joined:
5 months, 2 weeks ago
Email:
9********@qq.com

A beginner in bioinformatics.

Posts by Hughie

<prev • 11 results • page 1 of 2 • next >
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Comment: C: RNA-seq normalization methods for cross samples comparison?
... Sorry, I'm a beginner here, already accepted your kindly answer. Thank you again! ...
written 7 days ago by Hughie30
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Comment: C: RNA-seq normalization methods for cross samples comparison?
... Well, I see! Thank you ! ...
written 7 days ago by Hughie30
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Comment: C: RNA-seq normalization methods for cross samples comparison?
... Thank you! But, I'm thinking that TPM just measures relative expression, so ,if sampleA has a gene1 which has reads number much larger than the same gene1 of sampleB,(supoose 1000 vs 10),so,will this dramaticlly changed expression effect other genes because of 'relative'. ...
written 7 days ago by Hughie30
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RNA-seq normalization methods for cross samples comparison?
... Hello! Recently, I'm learning about RNA-seq quatification and I found there are many normalization methods, such as, CMP,RPKM/FPKM,TPM,TMM etc. After reading some papers about them, I noticed that all of these units mentioned above can't compare directly between samples because they just get relati ...
next-gen sequence rna-seq written 8 days ago by Hughie30 • updated 7 days ago by kennethcondon2007800
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Comment: C: Different trimming SLIDINGWINDOW threshold value mapping comparison
... Thanks! I'm gonna try Phred algorithm. ...
written 12 days ago by Hughie30
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Comment: C: Different trimming SLIDINGWINDOW threshold value mapping comparison
... Thanks Brain! I'm sorry to mistaken replying a wrong place below instead of commmenting your answer. ...
written 12 days ago by Hughie30
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Answer: A: Different trimming SLIDINGWINDOW threshold value mapping comparison
... Thanks! Brain Bushnell. Actually, I also used MINLEN:35 to discard the reads with length beneath 35 accroding an answer for my last post, I'm not sure whether this effected my results observably because actually I also trimmed my data before without using MINLEN(i.e keep all reads after trimming),I ...
written 12 days ago by Hughie30
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Different trimming SLIDINGWINDOW threshold value mapping comparison
... Hello! Recentlly, I trimmed my poor tail .fastq dataset using Trimmomatic's SLIDINGWINDOW parameter, in which I chose threshold value 15~30(i.e SLIDINGWINDOW:4:15~SLIDINGWINDOW:4:30). after, I mapped them using STAR, but I found with the increase of threshold, totally, unique and multiple mapped re ...
next-gen alignment rna-seq written 12 days ago by Hughie30
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Comment: C: How to choose Trimmomatic's parameter 'MINLEN '?
... Thanks, Ian! I'm gonna try MINLEN:35 for trimming. ...
written 14 days ago by Hughie30
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Comment: C: How to choose Trimmomatic's parameter 'MINLEN '?
... Ian, thank you very much! But I'm afraid if I set MINLEN:35, there are pretty many reads lost. Below, I post counts colected from one of my trimmed .fastq file: Read_length Read_num 10 2026 11 2334 12 1709 13 1421 14 1251 15 ...
written 14 days ago by Hughie30

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