User: Gary

gravatar for Gary
Gary480
Reputation:
480
Status:
Trusted
Location:
Taiwan/Taichung/China Medical University Hospital
Last seen:
2 weeks ago
Joined:
5 years, 1 month ago
Email:
y**********@gmail.com

Posts by Gary

<prev • 78 results • page 1 of 8 • next >
4
votes
2
answers
144
views
2
answers
The number of reads from the BMA file is more than the number of reads from its original FASTQ file
... 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 ...
fastq alignment rna-seq bam written 14 days ago by Gary480 • updated 14 days ago by h.mon29k
0
votes
1
answer
1.4k
views
1
answers
Comment: C: What sequences should I use for ATAC-Seq adapter trimming using trimmomatic 0.36
... 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 Gary480
0
votes
1
answer
1.4k
views
1
answers
Comment: C: What sequences should I use for ATAC-Seq adapter trimming using trimmomatic 0.36
... Many thanks for your information. ...
written 13 months ago by Gary480
5
votes
1
answer
1.4k
views
1
answer
What sequences should I use for ATAC-Seq adapter trimming using trimmomatic 0.36?
... 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 ...
trimmomatic trimming adapter atac-seq written 13 months ago by Gary480 • updated 13 months ago by h.mon29k
0
votes
1
answer
410
views
1
answers
Comment: C: A weird PCA result using a local Galaxy
... Many thanks to your super professional answer. ...
written 13 months ago by Gary480
5
votes
1
answer
410
views
1
answer
A weird PCA result using a local Galaxy
... 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 ...
galaxy pca rna-seq principal component analysis written 13 months ago by Gary480 • updated 13 months ago by Devon Ryan94k
0
votes
1
answer
694
views
1
answers
Comment: C: Duplicated ATAC-Seq peaks called by MACS2
... 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 Gary480
5
votes
2
answers
594
views
2
answers
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
... 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 ...
minmqs quantification featurecounts rna-seq written 14 months ago by Gary480 • updated 14 months ago by Gordon Smyth1.5k
0
votes
1
answer
694
views
1
answers
Comment: C: Duplicated ATAC-Seq peaks called by MACS2
... 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 Gary480
7
votes
1
answer
694
views
1
answer
Duplicated ATAC-Seq peaks called by MACS2
... 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 ...
macs peak calling macs2 atac-seq written 14 months ago by Gary480 • updated 14 months ago by geek_y10k

Latest awards to Gary

Great Question 11 months ago, created a question with more than 5,000 views. For How to modify a gff3 file for HTSeq?
Popular Question 11 months ago, created a question with more than 1,000 views. For ChIP-Seq contaminated by human tissue?
Scholar 11 months ago, created an answer that has been accepted. For A: 200 vs 400 bp Ion Torrent
Popular Question 12 months ago, created a question with more than 1,000 views. For ChIP-Seq contaminated by human tissue?
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Network analysis software
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: How is FDR calculated in MACS?
Great Question 2.7 years ago, created a question with more than 5,000 views. For How to modify a gff3 file for HTSeq?
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: How is FDR calculated in MACS?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For ChIP-Seq contaminated by human tissue?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to modify a gff3 file for HTSeq?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Macs2 callpeak error: IndexError: list index out of range
Popular Question 2.7 years ago, created a question with more than 1,000 views. For htseq-count cannot find pysam
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Error message produced by bowtie2 (HiC-Pro)
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to install bedClip on a Mac Book Pro?
Voter 3.1 years ago, voted more than 100 times.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For ChIP-Seq contaminated by human tissue?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Network analysis software
Popular Question 3.7 years ago, created a question with more than 1,000 views. For htseq-count cannot find pysam
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How to modify a gff3 file for HTSeq?
Scholar 4.8 years ago, created an answer that has been accepted. For A: 200 vs 400 bp Ion Torrent
Supporter 4.9 years ago, voted at least 25 times.
Scholar 5.0 years ago, created an answer that has been accepted. For A: 200 vs 400 bp Ion Torrent
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Network analysis software

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1072 users visited in the last hour