User: surjray

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surjray0
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Posts by surjray

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Question about X and Y chromosomes in Diffbind and how they are handled.
... Dear all,        We are using Diffbind to examine differential peak enrichment between male and female samples. Our input control is from the same sample before the immunoprecipitation stage. We have 4 replicates per treatment. The way we are using the Diffbind commands is exactly like given in the ...
diffbind written 3.6 years ago by surjray0 • updated 3.6 years ago by Gord Brown590
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Answer: A: easyRNASeq: "Error in IRangesList"
... Dear Nico,         I used the exact same annotation file with older versions of easyRNASeq and they worked fine. The latest version seems to be running into this error.         Thanking you. ...
written 4.2 years ago by surjray0
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easyRNASeq: "Error in IRangesList"
... Dear all,               I have been running easyRNASeq to count reads for RNA-Seq samples. However I ran into an error with the latest easyRNASeq version. Here is the command I used: fruMA_male_WCS_male_Unique.count.table <- easyRNASeq( filesDirectory = "./FruMA_Male_WCS_Male/tophat_BAM_files/" ...
easyrnaseq written 4.2 years ago by surjray0
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Error while reading in peaksets into DiffBind.
... Dear all,             I am trying to analyze ChIP-Seq data using DiffBind. After creating a CSV file with the experiment design and the peak files information. like shown in the DiffBind vignette, I used the following command to create a DBA object: H3K27ac_samples.dba = dba( H3K27ac_samples ) Ho ...
diffbind reading peaks written 4.4 years ago by surjray0 • updated 4.4 years ago by Gord Brown590

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