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Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC by James W. MacDonald 63k

If you essentially combined multiple BAM files in the MACS call, you could then just combine them using `samtools cat`, in which case you o…

Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k

I can rephrase your question as: Why is number of reads not the superior estimate for the scaling factor (the "m" in rpm). There are som…

Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0

Hi Michael, Yes I manually calculated the RPMs by dividing each genes RPM to the library read depth. I didn't do any other normalization …

Comment: shinyMethyl - saving the file by dorota.komar • 0

I tried printing the page as pdf, unfortunately I get the same problem. I guess for now, I will need to save the graphs separately :) Than…

Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by Mike Smith ★ 6.1k

I'll echo James' suggestion to use the GRCh37 mirror. Most mirrors only have a guaranteed lifetime of 5 years from Ensembl, although it se…

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Batch correction and Deseq2

A: Read counts between QSEA and MEDIPs

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