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Doubts with mash output

Hi everyone!

I am trying to learn GWAS and I am starting with the following tutorial:

https://pyseer.readthedocs.io/en/master/tutorial.html

This tutorial includes a set of pre-computed files. When I take a look at them, I understand and know how to produce every single one of them but one that is called mash_sketch which is supposed to be the result of running mash sketch -s 10000 -o mash_sketch *.fa

My problem is that I understand that sketching is done on individual files (contigs resulting from an assembly in this case) and thus getting an individual sketch output for each input. I don't understand why I am getting a single file in this downloadable content, I get the feeling that this is a merged file of all the sketches. Is that right? Can that be done?

Any help or explanation would be super appreciated.

Alan.

mash gwas
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written by SushiRoll • SushiRoll

I am answering to myself because I figured it can actually be done. My main problem right now is that *.fa is not being recognised as a wildcard for every fasta file so I have to manually use -in=xxxxx.fa -in=yyyyy.fa -in=zzzzzz.fa which is obviously not the right way. Could anyone help me solve this please? I am running this on Windows and not on Linux

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written by SushiRoll • SushiRoll

make sure to remove the trailing dot . in your pattern *.fa.

the bash patterns are applied and expanded into file names in bash

• 0 views • link
written by Istvan Albert Istvan Albert

Hi Istvan,

Thank you for your response, the . after *.fa is not actually there, it got there because of my habit of punctuating every sentence. I will edit it right away

• 0 views • link
written by SushiRoll • SushiRoll

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