User: gtechbio

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Posts by gtechbio

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DiffBind confuses coordinates of peaks
... Hi All, I'm analyzing ATAC-seq data and use MACS2 for peak calling and DiffBind for occupancy and affinity analysis. In occupancy analysis when I try to find peaks that are unique to one group, it seems that DiffBind confuses the contigs and coordinates of the peaks. For example I get,   SU68 ...
diffbind atacseq written 4 hours ago by gtechbio0
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Comment: C: Allele-specific expression with different gene lenghts
... Thanks for elaborating!Now it makes sense for me. And I guess for human data (i.e. patients or any "case-control" study) this "individualized" approach would matter compared to mine. In my case though I analyze yeasts (they are quite homogenous within the culture), so I can in principle assume that ...
written 4 months ago by gtechbio0
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Comment: C: Allele-specific expression with different gene lenghts
... Hi Michael, I am sorry for ignorance, but still I don't understand why my example wouldn't work properly: I specify in design formula that there are two conditions (basically parents), and I control for library size and gene length. So basically it will compare condition 1 vs condition 2, and will s ...
written 4 months ago by gtechbio0
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Comment: C: Allele-specific expression with different gene lenghts
... Dear Michael, Regarding normalization, so thanks a lot, I will try running the code like that. Regarding the count table, so for example SC1 and SU1 are from the same library (as other samples with the same numbers), and I thought my design will compare alt to ref, like you have mentioned, won't i ...
written 4 months ago by gtechbio0
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Comment: C: Allele-specific expression with different gene lenghts
... Dear Michael, I was wondering if in DESeq2 it is possible to simultaneously set size factors and control for gene length (like you have suggested in your post)? Thanks in advance ...
written 5 months ago by gtechbio0
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Comment: C: Allele-specific expression with different gene lenghts
... Hi Michael, Thanks for reply. Just to make sure I do everything in order: My `count_table` looks like SC1 SC2 SC3 SU1 SU2 SU3 YBR177C_Sbay_4.429 2711 3397 3765 1246 2156 3287 YIL140W_Sbay_9.48 178 111 204 109 271 250 Y ...
written 5 months ago by gtechbio0
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Allele-specific expression with different gene lenghts
... Hi, I want to use DESeq2 for assessing allele-specific expression. I will compare gene-level allelic counts of a yeast hybrid (basically comparing counts of orthologous genes of parentals of this hybrid). I'm aware of this tutorial http://rstudio-pubs-static.s3.amazonaws.com/275642_e9d578fe1f7a404aa ...
rnaseq deseq2 allele-specific-expression written 5 months ago by gtechbio0 • updated 5 months ago by Michael Love19k
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Comment: C: Time course DE analysis in DESeq2 with Wald test
... Thanks for your time Michael and sorry for coming back to you late. As far as I understand, with LRT the software will find a gene which became differentially expressed at any time point. In this case we assume, that if gene is changing its expression, this change is always towards one direction - ...
written 10 months ago by gtechbio0
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Comment: C: Time course DE analysis in DESeq2 with Wald test
... Hi Michael, thank you for your reply. Could you also please point out what is the conceptual difference between this approach and LRT-based time-course analysis, and whether any of those has advantages or disadvantages over another? And one more question regarding shrinkage (sorry if a silly one): ...
written 11 months ago by gtechbio0
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Time course DE analysis in DESeq2 with Wald test
... Hi All, This is to make sure I do a correct thing (which might be actually wrong). I have a time series experiment: 0 time point - yeast is growing alone (control), 3,12,24h time point - yeast is growing on human cells, and 24h (control) - yeast is growing alone. I need to do a time-series DE anal ...
deseq2 time-series written 11 months ago by gtechbio0 • updated 11 months ago by Michael Love19k

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