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

ADD COMMENTlink 17 months ago b10hazard • 20 • updated 17 months ago RamRS 21k
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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.

ADD REPLYlink 17 months ago
lakigigar
• 220
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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.

ADD COMMENTlink 17 months ago Rob 3.3k
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Thank you for the suggestion. I will give that a shot.

ADD REPLYlink 17 months ago
b10hazard
• 20

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