Doubts with mash output
0
0
Entering edit mode
8 weeks ago
alanxelena • 0

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 • 195 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1675 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6