Building salmon index #751
MarkiMarki
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Hello
I'm new to the field and recently started using Salmon (btw thank you for this wonderful library!).
In the "Getting started" page [https://combine-lab.github.io/salmon/getting_started/] there is a remark that I do not fully understand:
"When you are building a salmon index, please do not build the index on the genome of the organism whose transcripts you want to quantify, this is almost certainly not want you want to do and will not provide you with meaningful results".
The same page uses Arabidopsis as a reference and in the docs there is a link to this page [https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/]- which provides mouse as ref..
My question is when generating a decoy aware transcriptome- which ref should to use for when analyzing human data?
Is there any preferred one?
Thanks!
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