User: Biologist

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Biologist190
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Posts by Biologist

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Comment: C: How to extract required lines of particular chromosome from a gtf file?
... I actually didd `grep` like this `grep -w chr3 sample.annotated.gtf > chr3.gtf`. Could you please show me an example command ...
written 3 months ago by Biologist190
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How to extract required lines of particular chromosome from a gtf file?
... I have gtf file that starts like below: GL000008.2 StringTie transcript 19957 20594 . + . transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; xloc "XLOC_000001"; class_code "u"; tss_id "TSS1"; GL000008.2 StringTie exon 19957 20594 . + ...
gtf command rna-seq linux written 3 months ago by Biologist190 • updated 3 months ago by Ram32k
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Comment: C: Question regarding immature transcripts with Ribo-zero RNA-seq data
... I didn't ask about the pipeline...my question is I found immature transcripts in my data. I would like to know whether such data can be used for novel lncRNA detection. ...
written 4 months ago by Biologist190
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Problem with edgesfile into cytoscape for network plot
... I was using 30,000 protein-coding genes and lncRNAs for network construction on WGCNA. I have got 25 modules. And I'm interested in creating a network plot. I see that everyone is using cytoscape. So, I got the edges and nodes files with the following commands. genes = colnames(datExpr) dim ...
wgcna cytoscape rna-seq R written 8 months ago by Biologist190 • updated 8 months ago by andres.firrincieli1.1k
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Comment: C: Problem with differential analysis between two groups having low raw counts
... Thanks a lot for the information. Yes, actually when I took all the genes long with novel lncRNA transcripts and performed DEG analysis. And what I see is there re no novel lncRNA transcripts among DEGs I got. What I'm interested in is differentially expressed novel lncRNA transcripts. And ofcourse ...
written 10 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... @geek_y and @ATpoint Could you please check my below comment and tell me your opinion.thanq ...
written 10 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... Yes, I added `lib.size` for `cpm`. I'm afraid that we if I merge these novel transcripts with mRNA and Known lncRNAs, I won't be able to detect any novel differentially expressed transcripts. Because mRNAs are high expressed and lncRNAs are low expressed. I see that library sizes of the samples is ...
written 10 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... From the pipeline [lncRNApipe][1] I used, to detect novel lncRNAs....I found approx 10,000 novel lncRNA transcripts. And this is what I used with edgeR for GroupA vs GroupB comparison. Don't know what else I should use. [1]: https://github.com/biocoder/Perl-for-Bioinformatics/blob/master/NGS-U ...
written 10 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... These 10,000 lncRNA transcripts were novel transcripts in my analysis. So, yes I used `cpm` only. ...
written 10 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... I'm interested in only lncRNAs. I don't think it is wrong. ...
written 10 months ago by Biologist190

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Popular Question 3 months ago, created a question with more than 1,000 views. For Is logCPM expression data good for plottinng?
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