Can I use aletsch to assemble single bulk rnaseq sample?

[xiekunwhy]

Hi,

I found that aletsch is much faster than scallop2, I want to known if I can use it to assemble single bulk-rnaseq sample (or multiple bulk-rnaseq sample merged bam) instead of using scallop2 ?
Why or why not?

Best,
Kun

[shaomingfu]

Hi Kun,

Thank you for trying Aletsch; I am so sorry for the late response.

Yes, you can certainly assemble a single bulk RNA-seq sample; in this case, I would expect its accuracy to be comparable to that of Scallop2. When assembling multiple bulk RNA-seq samples, which is what Aletsch is designed for, I strongly recommend listing all samples directly in the input file, rather than merging them into a single bam.

Aletsch is multi-threaded and incorporates several optimizations, which likely explains why it's faster than scallop2.

Best,
Mingfu