Question: Tune Star Parameters For Transcriptome Assembly (Cufflinks)
gravatar for Nicolas Rosewick
7.5 years ago by
Belgium, Brussels
Nicolas Rosewick9.2k wrote:


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



assembly rna-seq transcriptome • 2.9k views
ADD COMMENTlink written 7.5 years ago by Nicolas Rosewick9.2k
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