User: Yonatan Amzaleg

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Posts by Yonatan Amzaleg

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Comment: C: DESeq2- preliminary study no replicates
... Thank you so much for your response. I'm a little confused as to how to perform the vst function without having run the DESeq function first? Should I run it with a design that works and then transform the data? Yonatan ...
written 8 months ago by Yonatan Amzaleg0
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DESeq2- preliminary study no replicates
... Hello, First off, I appreciate everyone reading this and providing insights. I'm aware what I'm asking is not statistically sound by any stretch of the imagination, however the current data I have is three samples (one replicate each). The conditions are such that two of the samples share a conditi ...
deseq2 error replicates deseqdatasetfrommatrix written 8 months ago by Yonatan Amzaleg0 • updated 8 months ago by Michael Love26k
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TCGAbiolinks specific mutation query
... Hello Everyone, I have a question about TCGAbiolinks that I didn't see anyone else address (please make me aware if I'm incorrect). My goal is to identify within TCGA-BRCA a specific mutation of interest and find all barcodes for breast cancer patients harboring this mutation and place it into a li ...
rnaseq tcga tcgabiolinks gdcquery mutation written 8 months ago by Yonatan Amzaleg0
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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 11 months 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 11 months 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 11 months 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 11 months 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 11 months ago by Yonatan Amzaleg0 • updated 11 months ago by Michael Love26k

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