User: Gary
Gary • 480
- Reputation:
- 480
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- Location:
- Taiwan/Taichung/China Medical University Hospital
- Last seen:
- 2 weeks ago
- Joined:
- 5 years, 1 month ago
- Email:
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Posts by Gary
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... Hi,
I have a FASTQ file (name as Origin_ELW24.fastq.gz) with 107,856,041 single-end 75bp reads. After trimming and alignment, we get a BAM file (name as ELW24.bam) via STAR. I use commands below to convert the BMA file to a new FASTQ file (name as New_ELW24.fastq.gz). The number of reads in the new ...
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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 13 months ago by
Gary • 480
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... Many thanks for your information. ...
written 13 months ago by
Gary • 480
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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 13 months ago by
Gary • 480
5
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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 13 months ago by
Gary • 480
• updated
13 months ago by
Devon Ryan ♦ 94k
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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 14 months ago by
Gary • 480
5
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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 14 months ago by
Gary • 480
• updated
14 months ago by
Gordon Smyth • 1.5k
0
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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 14 months ago by
Gary • 480
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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