Lately, I was playing a little bit with STAR and cufflinks to perform transcriptome assembly. I have a gtf file but it is not the best one (I study a non-well annotated species ). Here is the parameters I used for STAR. FYI, I have 2x50bp strand specific reads (~15 samples).
STAR --genomeDir $stargenomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignSJDBoverhangMin 1 --outFilterType BySJout --outFilterMismatchNmax 5 --readFilesIn $r1 $r2 --readFilesCommand zcat
and for cufflinks :
cufflinks -g $gtf -b $genomeFile -u --library-type fr-firststrand aligned.bam
After that, I want to merge the assembly using cuffmerge.
Anyone has advices to better tune STAR and cufflinks paramteres for transcriptome assembly ? or maybe other idea/tools to perform that on RNA-Seq data