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User: Gary

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Gary0
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Posts by Gary

<prev • 51 results • page 1 of 6 • next >
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Comment: C: The meaning of results produced by the bamQC function implemented in the ATACseq
... Hi Jianhong, Thanks a lot. May I have an additional question? Using ENCODE's terms and definitions for the ATAC-Seq library complexity, I don't understand why (1) my bottlenecking level is "Severe" based on my PBC1 value (0.6878547 < 0.7), but (2) my bottlenecking level is "None" base on my PCB2 ...
written 39 minutes ago by Gary0
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The meaning of results produced by the bamQC function implemented in the ATACseqQC
... Hi, I use bamQC in ATACseqQC to do the quality analysis of our ATAC-Seq data. However, I have some questions below. Could you help me? Many thanks. Best, Gary My questions (1) The meaning of $totalQNAMEs (2) The meaning of $nonRedundantFraction (3) The meaning of $MAPQ. Is it mapping quality? ...
atac-seq atacseqqc bamqc totalqnames mapq written 3 days ago by Gary0 • updated 1 day ago by Ou, Jianhong1.1k
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Julie, I appreciate your professional help very much. This time, I don't trim any sequence reads and use Bowtie2 with the very-sensitive-local parameter for the alignment. The percentage aligned reads are (1) 71.73% when I use Chinese bulbul genome only, (2) 10.92% when I use black-capped bul ...
written 3 days ago by Gary0
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Hi Julie, Thank you so much. Usually, I use the command below to remove reads aligned to mitochondria. samtools idxstats CTNNB1_G8_13.bam | cut -f 1 | grep -v chrM | xargs samtools view -b CTNNB1_G8_13.bam > CTNNB1_G8_13_woChrM.bam However, there are only 32 scaffolds, and no one is annot ...
written 11 days ago by Gary0
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How about our ATAC-Seq data quality analyzed by ATACseqQC
... Hi, We produced a test ATAC-Seq data with 26.8 million 87bp paired-end reads using Chinese bulbul's feathers. I used Bowtie2 for the alignment and ATACseqQC for the quality analysis. The below are (1) fragment size distribution and (2) library complexity produced by ATACseqQC. I think that we have ...
atac-seq atacseqqc quality analysis fragment size distribution library complexity written 11 days ago by Gary0 • updated 11 days ago by Julie Zhu4.0k
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Comment: C: The optimal minMQS parameter in featureCounts for RNA-Seq quantification
... Hi Wei Shi, Thank you so much. Your suggestion is very helpful. ...
written 15 days ago by Gary0
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The optimal minMQS parameter in featureCounts for RNA-Seq quantification
... I have asked this question on Biostars (https://www.biostars.org/p/361800/), and have not got any response. Many thanks for any suggestions and helps. We have six RNA-Seq data, including three wild type and three knock-out mice. I use STAR 2.5.3a (built-in Partek Flow) for the alignment and feature ...
featurecounts star rna-seq minmqs mapping quality score written 15 days ago by Gary0 • updated 15 days ago by Gordon Smyth36k
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How to color different column bars independently using dba.plotHeatmap (DiffBind)?
... Hi, I would like to color (1) the column bar of the antibody factor using "orange", "orchid1", and "mediumpurple1", (2) the column bar of the sex factor using "magenta", and "cyan". The commands I used and the figure I produced are below. Could you teach me how to perform it correctly? In addition, ...
diffbind dba.plotheatmap written 3 months ago by Gary0 • updated 3 months ago by Rory Stark2.7k
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Comment: C: Package is not available for R version 3.5.0
... It is working. Thanks a lot. May I know the difference between biocLite() and install.packages()? Thanks a gain. ...
written 7 months ago by Gary0
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Package is not available for R version 3.5.0
... Hi, Using qvalue as an exmple (the detail bleow), I cannot install it for R 3.5.0. It is the same for other packages I need. Anyone can help me? Many thanks. > require(NBPSeq) Loading required package: NBPSeq Error: package or namespace load failed for ‘NBPSeq’ in loadNamespace(j <- i[[1L]] ...
qvalue nbpseq written 8 months ago by Gary0 • updated 8 months ago by Gordon Smyth36k

Latest awards to Gary

Popular Question 7 months ago, created a question with more than 1,000 views. For Could not find function "makeTranscriptDbFromGFF"
Popular Question 7 months ago, created a question with more than 1,000 views. For DiffBind installation doesn't work
Supporter 17 months ago, voted at least 25 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to run the rpkm function of edgeR
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DiffBind installation doesn't work

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