User: divya.nandakumar

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Posts by divya.nandakumar

<prev • 16 results • page 1 of 2 • next >
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Comment: C: ChIP-Seq for viral genomes
... Thanks! I will check them out. I was also able to get some suggestions from the makers of HOMER to adjust the parameters for small genomes. ...
written 2 days ago by divya.nandakumar20
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Comment: C: Adjust width of annotations in pheatmap
... Thanks. I ended up using ComplexHeatmap. It had more options that I needed. ...
written 8 days ago by divya.nandakumar20
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Comment: C: Adjust width of annotations in pheatmap
... I went over the entire help section and also looked through the forums to see if this had been done with pheatmap and couldnt find anything. I spent quite some time (I am new to this) trying to figure out a heatmap function to draw multiple annotations. I was initially using heatmap.2 which allows f ...
written 10 days ago by divya.nandakumar20
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Adjust width of annotations in pheatmap
... Is there a way to adjust the width of row annotations in pheatmap? or are there heatmap programs that will allow for this? ...
R heatmap written 10 days ago by divya.nandakumar20
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Comment: C: ChIP-Seq for viral genomes
... I align to both the viral and host genome to avoid any mis alignments.. I then use only the viral aligned reads for peak analysis. Using the host+viral leads to a bunch of false positives from the host which look nothing like peaks on the genome browser and almost nothing from the virus which is whe ...
written 10 days ago by divya.nandakumar20
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Comment: C: ChIP-Seq for viral genomes
... The viral genome exists as episomes in the cell. It is not integrated in to the genome. ...
written 11 days ago by divya.nandakumar20
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Comment: C: Cut off for DE genes
... I am using DESeq2 for determining the log2FC and the fdr. Most of the viral genes that are down regulated are significant as seen by the fdr. Sorry if my questions wasnt clear but my question was of the ones that are significantly down-regulated, is there a statistic that I can use to say that one ...
written 11 days ago by divya.nandakumar20
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Cut off for DE genes
... Hi, I am using RNA Seq to identify genes that are down-regulated in a mutant cell line for a viral transcription factor compared to WT. The cell line has been infected with a virus and I am specifically interested in viral transcript down regulation. In the mutant cell line, almost all viral gen ...
rna-seq written 11 days ago by divya.nandakumar20 • updated 11 days ago by waqaskhokhar99910
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ChIP-Seq for viral genomes
... I am trying to analyze ChIP-Seq data from a viral transcription factor. I am interested in identifying peaks in the viral genome specifically (~150 kb). I am having a hard time calling peaks from programs like MACS2 or Homer using default settings and just changing the genome size. When I look at ...
next-gen chip-seq written 12 days ago by divya.nandakumar20
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Comment: A: Combining viral and host GTF files
... Thanks. It worked for me. ...
written 16 months ago by divya.nandakumar20

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