User: Gary
Gary • 450
- Reputation:
- 450
- Status:
- Trusted
- Location:
- Taiwan/Taichung/China Medical University Hospital
- Last seen:
- 3 months, 4 weeks ago
- Joined:
- 4 years, 6 months ago
- Email:
- y**********@gmail.com
Posts by Gary
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... Dear ATpoint,
Sure, I have quoted them. Many thanks for your help. However, I don't understand that I trimmed the TruSeq instead of the Nextera adapter. Could you explain it more clearly to me? Thank you so much.
Best,
Gary ...
written 5 months ago by
Gary • 450
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... Many thanks for your information. ...
written 5 months ago by
Gary • 450
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... Hi,
I want to use Trimmomatic 0.36 to trim ATAC-Seq adapter sequences. However, I am not sure which sequences I should use to trim our fastq files. Should I use the NexteraPE-PE.fa file provided by Trimmomatic 0.36 based on two Biostars threads below?
> Biostars thread I: The only odd thing I s ...
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... Many thanks to your super professional answer. ...
written 6 months ago by
Gary • 450
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... Hi,
We use a local Galaxy to run PCA (principal component analysis) based on six mouse RNA-Seq data. However, our result is weird: (1) PC1 can explain nearly all variation (94.5%); (2) All six samples on the 0.4 of PC1. Could you help us? Many thanks.
Best,
Gary
![enter image description here][1 ...
written 6 months ago by
Gary • 450
• updated
6 months ago by
Devon Ryan ♦ 91k
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... Hi geek_y, Many thanks for your suggestion. It is very helpful. Using the ChineseBulbulHead_peak_18a & 18b as an example (the figure below), I find that there are two sub-peaks. The first track is a bed file using MACS2 command below without the --call-summit parameter.
macs2 callpeak -t Ch ...
written 6 months ago by
Gary • 450
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... I have 6 mouse RNA-Seq data, and use STAR for the alignment and featureCounts for the quantification. The command I run featureCoutns is below.
rc <- featureCounts(files = c("Chuong753.bam", "Chuong754.bam", "Chuong755.bam", "Chuong756.bam", "Chuong757.bam", "Chuong758.bam"), annot.ext = "mm ...
written 6 months ago by
Gary • 450
• updated
6 months ago by
Gordon Smyth • 950
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... Hi, geek_y. Thank you so much. I rerun MACS2 without the --call-summits parameter and no subpeaks have the same peak boundaries. Do you mean it is because (1) I run the --call-summits parameter, (2) ATAC-Seq have many big peaks? However, I don't really understand the manual. Could you explain it mor ...
written 6 months ago by
Gary • 450
7
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... Hi,
I use MACS2 to do peak calling for ATAC-Seq data using the command below. However I found that some duplicated peaks called by MASC2, e.g. ChineseBulbulHead_peak_23a, ChineseBulbulHead_peak_23b, & ChineseBulbulHead_peak_23c (the detail below). I don’t meet the same problem before. Could you ...
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... Hi,
Could you help me about the bowtie2 error message below that I don’t understand? I run HiC-Pro (Servant et al., 2015) for our chicken HiChIP data (Mumbach et al., 2016) with 40bp paired-end reads. HiC-Pro is an aligner based on bowtie2. After running, bowtie2 showes error message below. Could y ...
written 2.2 years ago by
Gary • 450
• updated
21 months ago by
ashwinkelkar • 10
Latest awards to Gary
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5 months ago,
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For ChIP-Seq contaminated by human tissue?
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For A: How is FDR calculated in MACS?
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For How to modify a gff3 file for HTSeq?
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For A: How is FDR calculated in MACS?
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created a question with more than 1,000 views.
For ChIP-Seq contaminated by human tissue?
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For How to modify a gff3 file for HTSeq?
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For Macs2 callpeak error: IndexError: list index out of range
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For htseq-count cannot find pysam
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For How to install bedClip on a Mac Book Pro?
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