User: piyushjo
piyushjo • 310
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Posts by piyushjo
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C: STAR genome index Error
... In my experience, I have successfully generated index on my desktop machine which had 40 GB RAM. Are you running it on your cloud? I hope you have enough space in the drive. That's the only suggest Alex (the Creator) himself mentioned which did the trick. ...
written 7 days ago by
piyushjo • 310
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C: STAR genome index Error
... I don't think number of threads are issue, it will just make the program run faster. And I mentioned about the memory and not thread.
It could be that you don't have enough free space. Someone got the same error, probably due to less than 100GB space.
Look here:
https://github.com/alexdobin/STAR/i ...
written 7 days ago by
piyushjo • 310
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C: STAR genome index Error
... The command looks ok. Also 36 GB is enough. But try increase the memory, just for sake of it. Was there some problem in downloading the genome? Did you unzip it after downloading? ...
written 7 days ago by
piyushjo • 310
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... Its not cpm normalization where the count is divided to per million reads, it is more normalized with size factor, to convert non-normally distributed data to normally distributed data. As the data is normal distribution to begin with, may be the size factor is close to one! You can obtain the norma ...
written 8 days ago by
piyushjo • 310
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... As stated below, the counts after normalization looks similar to original counts due to normal distribution of the original data.
Also I normally prefer using vst normalized data for pca or any other processing (like WGCNA) ...
written 8 days ago by
piyushjo • 310
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... Why exactly you want to normalize counts by log2?
Can you also print output counts after normalization from DESeq2. ...
written 8 days ago by
piyushjo • 310
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... In my experience the recommended cutoff depends upon the data and is not a standard cut off for all data. You would have to set it depending where you see the knee in the distribution, the value just below it. ...
written 8 days ago by
piyushjo • 310
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... Doesn't the tutorial mention to use rlog or vst normalized values as input? ...
written 8 days ago by
piyushjo • 310
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Comment:
C: GSEA analaysis understaning
... It does not explain what is that gene ratio. In one figure it mentions gene ration and in second it mentions, genes affected by genes in the pathway geneset. I am sure you get a better enrichment values from GSEA analysis. I can only say that published resources are likely to be accepted more than i ...
written 9 days ago by
piyushjo • 310
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... Just as a caution, in my experience Seurat MultiCCA over-integrates the data. I have been advised to use fastMNN, that I also find to be a better alternative. ...
written 10 days ago by
piyushjo • 310
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created a question with more than 1,000 views.
For Creating interaction network using cytoscape
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created a question with more than 1,000 views.
For Hisat2 index building taking days even with 40 GB RAM
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created 100 posts.
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3 months ago,
created an answer with at least 3 up-votes.
For A: how do I split fastq from SRA?
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created a question with more than 1,000 views.
For How different is rlog transformation from vst transformation in DESeq2
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For A: Get a bunch of ENTREZID into gene symbols
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For How different is rlog transformation from vst transformation in DESeq2
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