-fr and -rf flags for strand specific RNA-seq

[asethi-1]

Hello,

I am mapping some paired-end strand-specific RNA-seq. This data maps logically with STAR, with the majority of reads in sense with their transcript. However, this is not the case in Magic-BLAST. Where can I find documentation on "-rf" and "-fr" flags for magic blast? How can they be used to achieve strand-specific mapping?

[boratyng]

Hi @asethi-1,

Thank you for giving Magic-BLAST a try. Unfortunately we do not currently have any documentation for -fr and -rf flags. At this time they only work with the SAM output. All alignments are still reported, but the "reads mapped and paired" flag is set for the alignments with the expected configuration.

What do you mean that STAR maps the reads logically and Magic-BLAST does not? Could you provide and example?

[asethi-1]

Thanks for your response. Although Magic-BLAST works great for some of my purposes (mapping to often repetitive intronic regions), the handling of stranded, paired RNA-seq data is a little challenging compared to other aligners.

What do you mean that STAR maps the reads logically and Magic-BLAST does not? Could you provide and example?

It appears that STAR can correctly flag reads from stranded RNA-seq libraries that are in the correct orientation. By default, magic-blast cannot do this.

[boratyng]

Thank you for reporting this. We need to do run a few comparisons between Magic-BLAST and STAR outputs to see what is happening. I will get back to you when we know more.