Hello,
I am new to programming/command line and am having trouble with the simplest of tasks I am sure. I am used to using Galaxy for analysis but I am trying to go towards programming/command line usage. I am trying to run cufflinks via command line but got the following error:
You are using Cufflinks v2.0.2, which is the most recent release.
Error: cannot open reference GTF file /--GTF for reading
Here is my input text into the command line(could have errors but I am not sure):
cufflinks -G/--GTF /Users/chriscard/Desktop/Galaxy2-\[UCSC_Main_on_Cow__all_mrna_\(genome\)\].gtf /Users/chriscard/Desktop/Galaxy14-\[Tophat_high_fert__accepted_hits\].bam o- /Users/chriscard/Desktop/Command_Line_Output
I plan on using tophat eventually as the first step to command line data analysis but for now I just tried to pull the .bam file from a tophat run off of one of my successful galaxy runs as well as the .gtf file for the reference mRNA that I want cufflinks to use(this is successful via Galaxy). Is there something wrong with my input text into command line? Do I need a different mRNA .gtf file? Sorry if this seems like a very simple task to be having problems with, trying to dive head first into this command line and coding stuff via a couple books I have started reading.
Thank You,
Chris
I am new to programming/command line and am having trouble with the simplest of tasks I am sure. I am used to using Galaxy for analysis but I am trying to go towards programming/command line usage. I am trying to run cufflinks via command line but got the following error:
You are using Cufflinks v2.0.2, which is the most recent release.
Error: cannot open reference GTF file /--GTF for reading
Here is my input text into the command line(could have errors but I am not sure):
cufflinks -G/--GTF /Users/chriscard/Desktop/Galaxy2-\[UCSC_Main_on_Cow__all_mrna_\(genome\)\].gtf /Users/chriscard/Desktop/Galaxy14-\[Tophat_high_fert__accepted_hits\].bam o- /Users/chriscard/Desktop/Command_Line_Output
I plan on using tophat eventually as the first step to command line data analysis but for now I just tried to pull the .bam file from a tophat run off of one of my successful galaxy runs as well as the .gtf file for the reference mRNA that I want cufflinks to use(this is successful via Galaxy). Is there something wrong with my input text into command line? Do I need a different mRNA .gtf file? Sorry if this seems like a very simple task to be having problems with, trying to dive head first into this command line and coding stuff via a couple books I have started reading.
Thank You,
Chris
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