User: Gary

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Gary20
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Posts by Gary

<prev • 64 results • page 2 of 7 • next >
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Julie, Thank you very much for your help. We will try the fixed cell number with a different amount of Tn5 enzyme. For sequence depth analysis (i.e., the number of peaks and total peak width), I used samtools and MACS2 commands below to remove (1) reads aligning to the black-capped bulbul mi ...
written 9 months ago by Gary20
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Comment: C: The meaning of results produced by the bamQC function implemented in the ATACseq
... Dear Julie, Your explanation is very helpful. Thank you so much. Best, Gary ...
written 9 months ago by Gary20
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Julie, Thank you so much. Below are the number of peaks and the total peak width of our ATAC-Seq sample (based on FDR < 10^-5). I think that we have to sequence more reads. Do you also think so? In addition, we only sequenced 26 million reads. May I know how do ATACseqQC extrapolate distinct fra ...
written 9 months ago by Gary20
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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 9 months ago by Gary20
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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 9 months ago by Gary20 • updated 9 months ago by Julie Zhu4.1k
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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 9 months ago by Gary20
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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 9 months ago by Gary20
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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 9 months ago by Gary20 • updated 9 months ago by Julie Zhu4.1k
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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 9 months ago by Gary20
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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 9 months ago by Gary20 • updated 9 months ago by Gordon Smyth39k

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