User: vinayjrao

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vinayjrao60
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Posts by vinayjrao

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Comment: C: Ballgown Error in file(file, "rt") : invalid 'description' argument
... You were right. That doesn't work either. ...
written 25 days ago by vinayjrao60
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Comment: C: Ballgown Error in file(file, "rt") : invalid 'description' argument
... The permissions to the gtf file is -rw-rw-r-- ...
written 25 days ago by vinayjrao60
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Comment: C: Ballgown Error in file(file, "rt") : invalid 'description' argument
... I used the absolute path. It's still the same :( ...
written 25 days ago by vinayjrao60
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Comment: C: Ballgown Error in file(file, "rt") : invalid 'description' argument
... I am using gtf files, whose field 9 contains gene_id ; transcript_id ; cov ; FPKM ; TPM ...
written 26 days ago by vinayjrao60
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Comment: C: Ballgown Error in file(file, "rt") : invalid 'description' argument
... Firstly, thanks for the reply. My working directory is the parent directory of ballgown, and as mentioned in the paper "Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown", the ballgown directory has a folder for each sample, within which my sample file wi ...
written 26 days ago by vinayjrao60
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Ballgown Error in file(file, "rt") : invalid 'description' argument
... Hi, I am trying out the new tuxedo protocol (hisat, stringtie and ballgown). While calling the ballgown function with `bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData=pheno_data)`, I get `Error in file(file, "rt") : invalid 'description' argument` Any help in this regard would ...
ballgown rna-seq written 26 days ago by vinayjrao60
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Comment: C: Data retrieval from GEO
... Hey, let's work with GSM85508 for example. Open https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM85508 and scroll down. You will find a label named "Series", beside which the GSE ID is mentioned. Click on the GSE ID, and at the bottom of the page, there will be a link to a compressed file. The ...
written 27 days ago by vinayjrao60
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Comment: C: Data retrieval from GEO
... Could you please give me a couple of those? ...
written 27 days ago by vinayjrao60
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Comment: C: Data retrieval from GEO
... Could you post the GSE ID. I'll try and get back to you. ...
written 27 days ago by vinayjrao60
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Comment: C: Installing old versions of cummeRbund
... I am currently learning the new tuxedo protocol, but the current analysis is for a colleague who wanted a vague idea for now, which will be analyzed better at a later point. So, I have got the differentially expressed genes, and want to plot the results using cummeRbund, for which I need your help i ...
written 4 weeks ago by vinayjrao60

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