User: Yonatan Amzaleg

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Posts by Yonatan Amzaleg

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Comment: C: DEseq2 for differential binding analysis ChIP seq
... Thank you @aaronlun for all your help, I successfully completed my first round of DB analysis! I am in the process of doing a different DB analysis and I was going to run it the same way, but I wanted to verify it with you first. In this case I'm comparing 4 different histone marks in three differe ...
written 10 days ago by Yonatan Amzaleg0
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Comment: C: Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 comb
... Yes, I've gotten this error too,  I tried to add "Chr" to the beginning of each chromosome in the bam file, but I then received another error  Error in mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",  :    sequence chrM has incompatible seqlengths:   - in 'x': 16569   ...
written 24 days ago by Yonatan Amzaleg0
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Comment: C: DEseq2 for differential binding analysis ChIP seq
... This is incredibly helpful, thank you so much!   So I'll merge the bam files and call the peaks against the merged inputs (I have an input for each condition), then I take that list produce a SAF file and run featureCounts to get a count table which I will then use in either DESeq2 or edgeR.  Am I ...
written 24 days ago by Yonatan Amzaleg0
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Comment: C: DEseq2 for differential binding analysis ChIP seq
... Thank you, Mike!   I saw in the paper you referenced by Aaron Lun they discuss pooling ChIP-seq libraries and calling peaks and using these "consensus peaks" as the regions by which we produce the count table, but I'm not so clear as to how to do this. By meaning do I take all conditions (ie, cond ...
written 25 days ago by Yonatan Amzaleg0
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DEseq2 for differential binding analysis ChIP seq
... Hello Everyone,   Let me start by saying I've read all posts that are similar to my question and the insights are tremendous! However, as I've been doing bioinformatics for a little over a year now, I'm still a newbie in all possible respects, and I just want a clarification.   So here's the gist. I ...
chipseq diffbind deseq2 csaw greylistchip written 4 weeks ago by Yonatan Amzaleg0 • updated 4 weeks ago by Michael Love21k

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