Hi,
I'm trying to set up a local version of Galaxy with all the NGS tools. I'm using this primarily for miRNA-seq data. So the workflow I'm using right now is:
FASTQ Groomer > Clipper > Map w/ Bowtie for Illumina > Filter SAM (for mapped) > Sort SAM for Cufflinks > Cufflinks
Now, this pipeline is working fine. I'm getting the 3 outputs from Cufflinks with FPKM etc. My question is this:
Is there a way in Cufflinks to generate "sequence-level" RPKM output from the SAM file? For example:
If I'm considering let-7a - my reads contain different versions/isoforms of different lengths:
let-7a --- TGAGGTAGTAGGTTGTATAGTT --- "x" RPKM
let-7a --- TGAGGTAGTAGGTTGTATAGT --- "y" RPKM
let-7a --- TGAGGTAGTAGGTTGTATAGTTT --- "z" RPKM
Can I get an output like the one above?
When I run Cufflinks on my Bowtie mapped SAM file, I get the FPKM counts for the miRNAs where - either all the isoforms mapping to the same miRNA are combined or only the most abundant isoform is considered (I'm not sure which). In any case, no sequences are reported in the Cufflinks output.
By the way, I'm mapping to miRBase hairpins.
Any suggestions (Cufflinks or otherwise) about getting this kind of output would be greatly appreciated.
Thanks!
Vivek
I'm trying to set up a local version of Galaxy with all the NGS tools. I'm using this primarily for miRNA-seq data. So the workflow I'm using right now is:
FASTQ Groomer > Clipper > Map w/ Bowtie for Illumina > Filter SAM (for mapped) > Sort SAM for Cufflinks > Cufflinks
Now, this pipeline is working fine. I'm getting the 3 outputs from Cufflinks with FPKM etc. My question is this:
Is there a way in Cufflinks to generate "sequence-level" RPKM output from the SAM file? For example:
If I'm considering let-7a - my reads contain different versions/isoforms of different lengths:
let-7a --- TGAGGTAGTAGGTTGTATAGTT --- "x" RPKM
let-7a --- TGAGGTAGTAGGTTGTATAGT --- "y" RPKM
let-7a --- TGAGGTAGTAGGTTGTATAGTTT --- "z" RPKM
Can I get an output like the one above?
When I run Cufflinks on my Bowtie mapped SAM file, I get the FPKM counts for the miRNAs where - either all the isoforms mapping to the same miRNA are combined or only the most abundant isoform is considered (I'm not sure which). In any case, no sequences are reported in the Cufflinks output.
By the way, I'm mapping to miRBase hairpins.
Any suggestions (Cufflinks or otherwise) about getting this kind of output would be greatly appreciated.
Thanks!
Vivek
Comment