User: gtechbio

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Posts by gtechbio

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Comment: C: DiffBind confuses coordinates of peaks
... Hi Rory, Thanks for reply! I tried using `DataType = DBA_DATA_FRAME`, but the problem persists and I still get contigs with strange coordinates. ...
written 5 weeks ago by gtechbio0
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Comment: C: DiffBind confuses coordinates of peaks
... Hi Rory, Thanks for reply. I use DiffBind_2.4.8. If you don't mind, I will send the SessionInfo to your email (the forum has character limitations). ...
written 6 weeks ago by gtechbio0
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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 7 weeks ago by gtechbio0 • updated 6 weeks ago by Rory Stark2.6k
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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 6 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 6 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 6 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 6 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 6 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 7 months ago by gtechbio0 • updated 7 months ago by Michael Love20k
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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 12 months ago by gtechbio0

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