Hi,
I am an undergraduate student in bioinformatics and I am looking for some advise on a project I am working on.
I have multiple samples from a cancer. The goal is to get the lncRNA and perform a differential expression analysis and find any correlation with the coding genes in the samples.
I have read multiple papers on the subject and I have constructed a pipeline to do this: bowtie-> cufflinks -> cuffmerge -> get lncRNA -> cuffdiff.
Can anyone provide some feedback on this pipeline?
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