Hello everybody!
Main question: with a minimal syntax like this
cufflinks -p 3 target.bam
what does cufflinks use to assembly the information contained in target.bam file?
I'd also like to know whether using a local reference (the fat 16GB+ files you can download from cufflinks website) cufflinks will name the transcripts with the gene names instead of CUFF.65279 and the like.
I'm a wet biologist trying to learn some bioinformatics. I managed to use bwa and picard to process the raw Illumina reads and get to a .bam file, and now I'm trying to learn how get some DE data out of my samples, but I hadn't found any tutorial clear enough to explain what cufflinks is actually doing. This is also why my thoughts are hazy and my questions are -probably- not outstanding.
Thank you for yuor help and support, as well as anyone who wrote some beautiful tutorials on SEQwiki.
Main question: with a minimal syntax like this
cufflinks -p 3 target.bam
what does cufflinks use to assembly the information contained in target.bam file?
I'd also like to know whether using a local reference (the fat 16GB+ files you can download from cufflinks website) cufflinks will name the transcripts with the gene names instead of CUFF.65279 and the like.
I'm a wet biologist trying to learn some bioinformatics. I managed to use bwa and picard to process the raw Illumina reads and get to a .bam file, and now I'm trying to learn how get some DE data out of my samples, but I hadn't found any tutorial clear enough to explain what cufflinks is actually doing. This is also why my thoughts are hazy and my questions are -probably- not outstanding.
Thank you for yuor help and support, as well as anyone who wrote some beautiful tutorials on SEQwiki.
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