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How to export the SNPs between whole genome alignments using the command line?

I am using Mauve to align two the whole genome sequences, one of the sequence is in the form of contigs. Another one is in the form of a complete genome.

I could align the two sequences using the following command

progressiveMauve ref.fa contigs.fa --output alignment.xmfa

And to extract the SNPs, I tried the solution from https://bioinformatics.stackexchange.com/questions/3658/can-i-export-the-snps-between-whole-genome-alignments-using-the-command-line/3664#3664

But while exporting the classpath path it shows an error

export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH"
find: ‘‹/home/me/Downloads/mauve_snapshot_2015-02-13/›’: No such file or directory

I have downloaded the mauve file and extracted it in the following location

/home/me/Downloads/mauve_snapshot_2015-02-13/

I am using a linux machine. How can I solve this issue?

mauve alignment sequence-alignment variant snp
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updated by h.mon h.mon • written by Paul Paul

1 answer

How did you define $MAUVE_DIR? The error message says:

find: ‘‹/home/me/Downloads/mauve_snapshot_2015-02-13/›’: No such file or directory

Which means you are defining $MAUVE_DIR as ‹/home/me/Downloads/mauve_snapshot_2015-02-13/›, but it should be /home/me/Downloads/mauve_snapshot_2015-02-13/ instead.

• 1 views • link
written by h.mon h.mon

Thanks a lot @h.mon :) it worked...

• 1 views • link
written by Paul Paul

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