lncRNA study pipeline using STAR

rajeev.vikram · 01-04-2016, 10:45 PM

Hi,

My Background:
I am new to NGS/RNA-seq and have been doing some background research. Now I suppose I have the basic theoretical knowledge and some specific questions, which I hope someone could help me with.Although I have used bioinformatics tools extensively, I dont have any programming experience.

My workstation: 120g ssd/3 -TbHDD/16gRAM(upgrading to 32g)/6 core processor/OS: Bio-Linux 8.

My Aim: To Identify and analyze lncRNAs from Stem cells of specific cell sub population. I want to generate a pipeline for lncRNA identification using STAR (not TOP-Hat/I am aware of the Tuxedo Suit though).

I really dont know how to go about this, I could not find a pipeline using STAR specifically for the purpose. Any suggestions or tutorial links will be very helpful. Also, any great places to download stem cell/cancer cell RNA-Seq (fastq) files??

kongantik · 02-03-2016, 08:23 AM

Hi,

You can use the pipeline I wrote to identify any putative novel lncRNAs. Use the pipeline from identification stage if you do not want to use Tuxedo protocol.

https://git.io/vgmsy

rajeev.vikram · 04-11-2016, 08:33 PM

Hi,
Thanks for your reply, I have gone through your lncRNApipe pipeline, however, when installing (I am trying to install in a custom directory, I am getting error with IO:Routine installation.
My System: Bio Linux on Ubuntu 14.04

Installation Command:

curl -Ok https://raw.githubusercontent.com/bi...ils/lncRNApipe
perl lncRNApipe --setup

Error Log:

We definetely need the custom module, IO::Routine.

Attempting to fetch IO::Routine from Perl-for-Bioinformatics repository on github...
mkdir: cannot create directory ‘/drive3/xyz’: File exists
mkdir: cannot create directory ‘Softwares/lncRNApipe/.build’: No such file or directory

.build dir ... FAIL

Can you please suggest an alternate or the reason for the error? or if you have any specific compilation technique for IO::Routine, please advice.
PS: I have never used perl.

Cheers

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01-04-2016, 10:45 PM	#1
rajeev.vikram Junior Member Location: Taipei Join Date: Aug 2015 Posts: 6	lncRNA study pipeline using STAR Hi, My Background: I am new to NGS/RNA-seq and have been doing some background research. Now I suppose I have the basic theoretical knowledge and some specific questions, which I hope someone could help me with.Although I have used bioinformatics tools extensively, I dont have any programming experience. My workstation: 120g ssd/3 -TbHDD/16gRAM(upgrading to 32g)/6 core processor/OS: Bio-Linux 8. My Aim: To Identify and analyze lncRNAs from Stem cells of specific cell sub population. I want to generate a pipeline for lncRNA identification using STAR (not TOP-Hat/I am aware of the Tuxedo Suit though). I really dont know how to go about this, I could not find a pipeline using STAR specifically for the purpose. Any suggestions or tutorial links will be very helpful. Also, any great places to download stem cell/cancer cell RNA-Seq (fastq) files??

02-03-2016, 08:23 AM	#2
kongantik Junior Member Location: central Join Date: Jan 2011 Posts: 9	Hi, You can use the pipeline I wrote to identify any putative novel lncRNAs. Use the pipeline from identification stage if you do not want to use Tuxedo protocol. https://git.io/vgmsy

04-11-2016, 08:33 PM	#3
rajeev.vikram Junior Member Location: Taipei Join Date: Aug 2015 Posts: 6	Hi, Thanks for your reply, I have gone through your lncRNApipe pipeline, however, when installing (I am trying to install in a custom directory, I am getting error with IO:Routine installation. My System: Bio Linux on Ubuntu 14.04 Installation Command: curl -Ok https://raw.githubusercontent.com/bi...ils/lncRNApipe perl lncRNApipe --setup Error Log: We definetely need the custom module, IO::Routine. Attempting to fetch IO::Routine from Perl-for-Bioinformatics repository on github... mkdir: cannot create directory ‘/drive3/xyz’: File exists mkdir: cannot create directory ‘Softwares/lncRNApipe/.build’: No such file or directory .build dir ... FAIL Can you please suggest an alternate or the reason for the error? or if you have any specific compilation technique for IO::Routine, please advice. PS: I have never used perl. Cheers