Hi, I am a very fresh man in analyzing the RNA-seq results; my questions are may be too long, but I really appreciate any of the helps.
Basically, we are comparing gene expression changes and I decided to use Cufflinks pipline for this purpose. Please first help to go through our procedure:
1) RNA-seq data from Illumina;
2) TOPHAT alignment to produce SAM files;
3) Cufflinks package to process SAM to estimate the gene expression levels;
Secondly, I have questions about annotation reference file,
1) where I could get it? I heard it is GTF format, and I already got a file from UCSC table browser, and I chose total human all mRNA for my case, is this right way?
2) Cufflinks has the option using annotation reference, so I could use GTF file I got from UCSC?
3) I read some threads here, and it seems Cufflinks contains some reference file itself?
4)could I easily get expression results referred with Gene ID/Symbol? Should I use Cuffcompare or Cuffdiff for my purpose to compare expression changes of genes in different samples.
Millions millions thanks!
Basically, we are comparing gene expression changes and I decided to use Cufflinks pipline for this purpose. Please first help to go through our procedure:
1) RNA-seq data from Illumina;
2) TOPHAT alignment to produce SAM files;
3) Cufflinks package to process SAM to estimate the gene expression levels;
Secondly, I have questions about annotation reference file,
1) where I could get it? I heard it is GTF format, and I already got a file from UCSC table browser, and I chose total human all mRNA for my case, is this right way?
2) Cufflinks has the option using annotation reference, so I could use GTF file I got from UCSC?
3) I read some threads here, and it seems Cufflinks contains some reference file itself?
4)could I easily get expression results referred with Gene ID/Symbol? Should I use Cuffcompare or Cuffdiff for my purpose to compare expression changes of genes in different samples.
Millions millions thanks!
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