Thank you for the suggestion. I will give that a shot.
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Will Kallisto or Salmon perform streaming alignment from the Sequence Read Archive?
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!
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1 answer
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.
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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.
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/