User: haibol

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haibol60
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Posts by haibol

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Comment: C: ATACseqQC function bamSplit returns error when input .bam is from mouse
... Hello, If you check the document for the function splitBam, you will see: splitBam(bamfile, tags, index = bamfile, outPath = NULL, txs, genome, conservation, positive = 4L, negative = 5L, breaks = c(0, 100, 180, 247, 315, 473, 558, 615, Inf), labels = c("NucleosomeFree", "inter1", "mononu ...
written 6 weeks ago by haibol60
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Comment: C: ATAC-QC shiftGAlignmentsList function
... Shuang, did you use the mm10 reference genome from the same source, such as NCBI, UCSC Genome Browser or Ensembl, to do alignment and the ATACseqQC analysis? I don't think ATACseqQC is species-aware. Haibo ...
written 8 weeks ago by haibol60
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Comment: C: ATAC-QC shiftGAlignmentsList function
... Shuang, did you use the mm10 reference genome from the same source, such as NCBI, UCSC Genome Browser or Ensembl, to do alignment and the ATACseqQC analysis? I don't think ATACseqQC is species-aware. Haibo ...
written 8 weeks ago by haibol60
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Hello Gary, You new plots based on filtered BAM looks better: many spiky peaks due to duplicates are gone. But you still missing the 38-100bp fragments, which was permanently removed by previous wet lab steps. A good tutorial for analyzing ATAC-seq data is here: https://informatics.fas.harvar ...
written 6 months ago by haibol60
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Hello Gary, You can find the scripts for filtering the unwanted reads from the supplementary file 1. Here are some script excerpts: #!/bin/bash #BSUB -n 8 # minimal numbers of processors required for a parallel job #BSUB -R rusage[mem=16000] # ask for memory 16G #BSUB - ...
written 6 months ago by haibol60
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Hello Gary, Yes, I agree with you that there is no or very few mitochondrial DNA sequence in the Chinese bulbul genome assembly. Haibo ...
written 6 months ago by haibol60
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Gary, Your command did not remove mitochondrial read alignment; it only output mitochondrial read alignments. One thin you can do is to do blast by using the black-capped bulbul mitochondrial genome as query to find out whether there is mitochondrial genome assembly in the draft genome assembly. ...
written 6 months ago by haibol60
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Comment: C: How about our ATAC-Seq data quality analyzed by ATACseqQC
... Hello Gary, I am one of the co-developer of the ATACseqQC package. Your library fragment size plot is not optimal. It lacks fragments less than 100bp, which should be from OPEN chromatin regions. On the other hand your plots did not show a apparent ladder pattern of mono-,bi-, tri-,...nucleos ...
written 6 months ago by haibol60

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