Will Kallisto or Salmon perform streaming alignment from the Sequence Read Archive?

Question

[b10hazard]

Do either Kallisto or Salmon have the ability to align data streamed from the Sequence Read Archive (SRA). Like what HISAT2 can do with the --sra-acc option?

Thanks!

[Lior Pachter]

You can see an example of a snakemake script to do this with kallisto here: [https://github.com/pachterlab/bears_analyses] Not streaming but could be modified to do so.

[Lior Pachter]

There is a blogpost describing how to do this for single-cell RNA-seq here: https://sinabooeshaghi.com/2019/07/09/fasterq-to-count-matrices-for-single-cell-rna-seq/

Answer 1

[Rob]

There is no option in salmon directly equivalent to the --sra-acc option in HISAT. However, salmon will happily accept streaming input from a fifo or named pipe. Hence, it should be possible to create a bash / snakemake / nextflow script to do the conversion and feeding of the reads directly to salmon so that you don't have to have the intermediate files sitting on your disk.

[b10hazard]

Thank you for the suggestion. I will give that a shot.