I have been trying to run tophat and cufflinks on Prochlorococcus genome (marine cyanobacteria). I am working using Galaxy; I am not a Linux user but rather a "wet' biologist trying to get into bioinformatics on my own).
I used the FASTA format of the genome available on MicrobesOnline: http://www.microbesonline.org/cgi-bi....cgi?tId=59919
I used a gtf file that the microbesonline people helped me create from the tab delimited version available on their website.
However, I am getting FPKMs of zero for everything.
I wasnt sure whether there is some disconnect between the genome and transcriptome files I am using, or whether the problem is that I am using a regular FASTA genome but not a bowtie index, or something else??? I would really appreciate troubleshooting help as there is very little help out there for people working on non-UCSC organisms!
I used the FASTA format of the genome available on MicrobesOnline: http://www.microbesonline.org/cgi-bi....cgi?tId=59919
I used a gtf file that the microbesonline people helped me create from the tab delimited version available on their website.
However, I am getting FPKMs of zero for everything.
I wasnt sure whether there is some disconnect between the genome and transcriptome files I am using, or whether the problem is that I am using a regular FASTA genome but not a bowtie index, or something else??? I would really appreciate troubleshooting help as there is very little help out there for people working on non-UCSC organisms!
Comment