Question: How to export the SNPs between whole genome alignments using the command line?
1
gravatar for ppurkayastha2010
3 months ago by
ppurkayastha201030 wrote:

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?

ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by ppurkayastha201030
2
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

We can help at this forum with Galaxy questions, so it might be best to ask this question back at bioinfo stackexchange channel or maybe a coding or OS channel/forum?

That said, if you did want to use Galaxy for this tool, there are two wrappers:

It isn't offered at any of the usegalaxy.* public servers but you could check the others linked below, or install the tool into your own Galaxy.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
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