User: piyushjo
piyushjo • 70
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Posts by piyushjo
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Comment:
C: how do I split fastq from SRA?
... if it was paired end it would be split, if the readings weren't paired they won't split. ...
written 4 weeks ago by
piyushjo • 70
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... use the following format
I have used it and it works for me
fastq-dump --origfmt --gzip --split-files SRR565555 (example SRR or ERR) ...
written 4 weeks ago by
piyushjo • 70
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... I have used minet and aracne (cytoscape plugin). You can read the revised ARACNE-AP paper for java script module
https://www.ncbi.nlm.nih.gov/pubmed/27153652
You can also use WGCNA approach.
https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ ...
written 5 weeks ago by
piyushjo • 70
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... Hi Erin!
I tried using the mouse id ENSMUSG00000097336. This is for mouse gene Fendrr. A human lncRNA FENDRR also exists, but when I try to search for it it doesn't show it. I also see that on the ensembl page the ortholog block doesn't get activated in Comparative genomics section. ...
written 6 weeks ago by
piyushjo • 70
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... Not working for long noncoding RNAs. :( ...
written 6 weeks ago by
piyushjo • 70
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... Hi,
I want to know if there is an easy way to find if a particular gene id (ensembl) is conserved between human and mouse. For individual genes I can try blast, but I actually have 3000+ genes (lncRNA), and I want to know what is the status of conservation and what is its human counterpart gene id. ...
written 6 weeks ago by
piyushjo • 70
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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 7 weeks ago by
piyushjo • 70
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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 7 weeks ago by
piyushjo • 70
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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 7 weeks ago by
piyushjo • 70
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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 7 weeks ago by
piyushjo • 70
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