User: piyushjo

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piyushjo70
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Posts by piyushjo

<prev • 41 results • page 1 of 5 • next >
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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 piyushjo70
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Answer: A: how do I split fastq from SRA?
... 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 piyushjo70
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Comment: C: DE Gene List to Regulatory Network
... 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 piyushjo70
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Comment: C: Conservation between mouse and human genes: form ensembl gene id?
... 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 piyushjo70
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Comment: C: Conservation between mouse and human genes: form ensembl gene id?
... Not working for long noncoding RNAs. :( ...
written 6 weeks ago by piyushjo70
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Conservation between mouse and human genes: form ensembl gene id?
... 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. ...
ensembl gene conservation written 6 weeks ago by piyushjo70
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How comprehensive is genode lncrna anotation for mouse?
... 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 ...
mouse gencode lncrna written 7 weeks ago by piyushjo70
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Comment: C: Is it okay to remove uncharacterised transcripts from downstream analysis in RNA
... 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 piyushjo70
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Comment: C: Proper design for DESeq2 and other RNAseq general questions
... 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 piyushjo70
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Tips for network prediction: WGCNA vs ARACNE (or MINET)
... 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 ...
wgcna network inference aracne written 7 weeks ago by piyushjo70

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