User: Gary

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Gary20
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4 years, 6 months ago
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Posts by Gary

<prev • 64 results • page 1 of 7 • next >
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Comment: C: How to produce the fraction of reads in peaks (FRiP) using DiffBind
... Hi Rory, Many thanks. Here you are. [http://68.181.92.180/~Gary/temporal/20190325_DiffBind_ATACseq_FRiP/dba_atac_peaks.RData][1] [http://68.181.92.180/~Gary/temporal/20190325_DiffBind_ATACseq_FRiP/dba_atac_counts.RData][2] By the way, I find that DiffBind can estimate FRiP values based on bam fi ...
written 8 months ago by Gary20
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Comment: C: How to produce the fraction of reads in peaks (FRiP) using DiffBind
... Hi Rory, Thank you very much. Below are their bam, bai, narrowPeak, and CSV files. Is it OK? Could you teach me the command lines how to save the DBA object (atac) before and after the call to dba, count()? After that, I can provide the files you need. Thank you very much. [http://68.181.92.180/~G ...
written 8 months ago by Gary20
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Enough cell number or not based on library complexity evaluation by ATACseqQC?
... Hi, I use ATACseqQC to estimate the library complexity of one ATAC-Seq data. When I don't trim any reads, it seems that our library complexity (cell number) is not enough because of a saturation plateau (fig. 1). However, it appears that the library complexity (cell number) is enough because of an ...
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How to produce the fraction of reads in peaks (FRiP) using DiffBind
... Hi, We have three mouse ATAC-Seq data. However, there is an error message when I would like to estimate their FRiP values using DiffBind below (i.e., Error in if (colnames(res)[i] == "Peak caller") { : argument is of length zero). Could you help me? Many thanks. Best, Gary > sessionInfo() ...
diffbind dba.count atac-seq frip dba.show written 8 months ago by Gary20 • updated 8 months ago by Rory Stark3.0k
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Haibo, Now I can run your command helped by my local friend (the detail below). However, we still don't understand the sub-command: awk 'BEGIN{FS=OFS="\t"} function abs(v) {return v < 0 ? -v : v}; /^@/. Does it mean that it removes duplicate reads in a BAM file? Many thanks for your kindly ...
written 9 months ago by Gary20
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Haibo, I really appreciate your help in resolving our ATAC-Seq problem. The information you provided is very helpful. I totally agree with you that I have to learn more about the Samtools, awk, and Unix commands. Hopefully, I can use your command correctly in the near future. Thank you once ag ...
written 9 months ago by Gary20
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Julie and Haibo, Thank you for your very useful help. I am not sure whether you saw my responses. I integrate my additional questions below. Could you help me again? Many thanks. After removing mitochondrial reads, duplicated reads, and other alignments of no interest (the partial bamQC resul ...
written 9 months ago by Gary20
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Haibo, After removing mitochondrial reads, duplicated reads, and other alignments of no interest (the partial bamQC results below), I reproduce the fragment size distribution and library complexity plots below. The library complexity profile is very different. Based on them, could you help to ...
written 9 months ago by Gary20
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Haibo, Thank you for your very useful information. I have not removed duplicated reads in the fragment size distribution and library complexity figures. We didn't make a size selection but used a Qiagen MinElute PCR Purification Kit for the purification as suggested by Buenrostro, et al. (201 ...
written 9 months ago by Gary20
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Dear Haibo, Many thanks for your suggestion and information. I have tried blast on the web, but it doesn't work (the figures below). Maybe the file size is too large, and I have to try a standalone blast. But it needs more time for me to learn how to install and run a standalone blast. ![enter ima ...
written 9 months ago by Gary20

Latest awards to Gary

Popular Question 13 months ago, created a question with more than 1,000 views. For How to run the rpkm function of edgeR
Popular Question 13 months ago, created a question with more than 1,000 views. For How to use DiffBind to get consensus peaks I am interested in?
Popular Question 17 months ago, created a question with more than 1,000 views. For Could not find function "makeTranscriptDbFromGFF"
Popular Question 17 months ago, created a question with more than 1,000 views. For DiffBind installation doesn't work
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to run the rpkm function of edgeR
Popular Question 3.0 years ago, created a question with more than 1,000 views. For DiffBind installation doesn't work

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