User: Peng Huang

gravatar for Peng Huang
Peng Huang50
Reputation:
50
Status:
Trusted
Location:
China/HangZhou/ZheJiang University
Last seen:
2 years, 4 months ago
Joined:
4 years, 10 months ago
Email:
2*********@qq.com

Posts by Peng Huang

<prev • 6 results • page 1 of 1 • next >
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Comment: C: trinitry Virusfinder error message no contigs
... I did the same thing and still get the same error, but I found it might due to the too high value of "thread_no" setted in the configure file. (actually, for sample input, it works at 8 threads but failed at 32 threads) ...
written 2.4 years ago by Peng Huang50
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Why HISAT2 gave low concordantly aligned pair rates for some samples while high for others with same options?
... Hi, everyone! Recently, I’m analyzing a transcriptomic dataset compromised of 66 RNA-seq samples (pair-end, 150bp, average depth 60M reads). After adapter cutting and low quality reads trimming by using Cutadapt and Trimmomatic respectively, read alignment was conducted by using the newest version ...
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The comparison between HISAT2 and Tophat2
... Hi, everyone! I just used HISAT to analyze a human HCC RNA-seq dataset, and I compared those alignment summaries with those of Tophat2, and found some interesting difference: **HISAT2 with almost default parameters except `--no-discordant`, using `genome_snp_tran` index provided in HISAT2 website* ...
tophat2 rna-seq hisat2 written 4.8 years ago by Peng Huang50 • updated 2.2 years ago by RamRS30k
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Comment: C: Could HISAT2-build build Hierarchical Graph FM index (HGFM) for a reference geno
... Yes, I know what you mean, I just saw the description for the option `----known-splicesite-infile` before I wrote this post, because it said: "Note that it is better to use indexes built using annotated transcripts (such `as_genome_tran` or `genome_snp_tran`), which works better than using this opt ...
written 4.8 years ago by Peng Huang50 • updated 2.2 years ago by RamRS30k
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Could HISAT2-build build Hierarchical Graph FM index (HGFM) for a reference genome plus transcripts for Rat (for example, Rn6)
... Hello everyone! I am doing rat RNA-seq analysis, previously using tophat2, as HISAT2 is a successor for tophat2, I plan to switch to it. And no pre-built indexs exist for Rat, hence I am going to build manually but I am wondering is it necessary and available to build Hierarchical Graph FM index (HG ...
hisat2 rna-seq transcriptome written 4.8 years ago by Peng Huang50 • updated 4.8 years ago by Devon Ryan97k
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Answer: A: HISAT (Transcript Alignment) and StringTie (Transcript Assembly)
... I am using Tophat2 + StringTie, compared with Cufflinks, StringTie seems to find more genes and transcripts expressed. That's all I could know till now.  ...
written 4.8 years ago by Peng Huang50

Latest awards to Peng Huang

Appreciated 4.3 years ago, created a post with more than 5 votes. For The comparison between HISAT2 and Tophat2
Great Question 4.3 years ago, created a question with more than 5,000 views. For The comparison between HISAT2 and Tophat2
Student 4.3 years ago, asked a question with at least 3 up-votes. For The comparison between HISAT2 and Tophat2
Popular Question 4.7 years ago, created a question with more than 1,000 views. For The comparison between HISAT2 and Tophat2

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