User: piyushjo
piyushjo • 40
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Posts by piyushjo
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... Hi,
I am working on a small paper to characterize lncrna in in vitro differentiated neural cells. I started with using gencode annotation file for quantifying lncRNA. Now I came across with several papers suggesting how to find novel lncRNA (lincScore). But then I realized that I am interested in w ...
written 1 day ago by
piyushjo • 40
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... I think for the enrichment part you can chose these annotated genes. Even if you had known genes, with unknown functions, you can still do GO analysis and its fairly acceptable. In my experience when I put my genes in DAVID for analysis, it doesn't recognize some IDs and discard it. These IDs could ...
written 5 days ago by
piyushjo • 40
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... Stringtie has a prepDY.py script that takes .gtf and converts into reads. I am not entirely sure of the algorithm used, but I use those counts for DESeq2 analysis. ...
written 5 days ago by
piyushjo • 40
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... Hi!
I am planning to do some network analysis using WGCNA and MINET (that also uses aracne algorithm). From my understanding WGCNA is pure correlation while aracne uses special algorithm (DPI) to find direct transcriptional relation. My thought was to first use WGCNA to find highly correlated genes ...
written 5 days ago by
piyushjo • 40
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... Hi,
I am trying to normalize RNA-Seq using DESeq2. I went on their website and they have three different transformations out of which I tried vst (variance stabilization transformation) and rlog. The thing is that if I have only sample per condition so vst didn't work in those cases but rlog did. Co ...
written 5 days ago by
piyushjo • 40
• updated
4 days ago by
Charles Warden ♦ 5.2k
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... Hi,
I am trying to find a definitive answer to my problem: shall I use annotation file to make a genome index or not?
In a bioinformatics workshop I attended the instructor said there is no fall out of not using the annotation file while making the index. I am aware that hisat2 website provides pre ...
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... Hi Genomax,
After talking to another bioinfo prof, he recommended me removing the overrepresented sequences as the source is tissue and not amplified RNA. Could you suggest any tool that can look and remove overrepresented sequences?
Thanks! ...
written 19 days ago by
piyushjo • 40
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... The DeSeq2 normalizes counts with respect to library size. So in principal it should be able to compare different sequencing runs together even with different library sizes. ...
written 20 days ago by
piyushjo • 40
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Comment:
C: Multiple probe for same gene
... It depends what is you end goal? Comparing gene expression among various condition of all the genes or just the gene of your focus? If you want to focus on all genes, just follow the procedure to merge different probe information into one. You could chose media, mean or just the highest. Like I said ...
written 20 days ago by
piyushjo • 40
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Comment:
C: Multiple probe for same gene
... https://www.biostars.org/p/47421/
https://www.biostars.org/p/74687/
https://support.bioconductor.org/p/92128/
Please refer to the following post to gain more information. I think different people might suggest different way, all equally correct/incorrect. Just be consistent, that should be the rule ...
written 20 days ago by
piyushjo • 40
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