psmc bootstrapping help
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3.2 years ago

Hi all,

I'm having trouble bootstrapping with psmc. I am able to run the analysis without bootstrapping and generate the plot, but I can't seem to get it going correctly with bootstrapping. I'd like to do 100 replicates.

Here's the code I've tried: seq 100 | xargs -P 6 psmc -N25 -t15 -r5 -p "4+25*2+4+6" -b -o s2863.split.psmc split.psmcfa

I've also tried this from the tutorial online: utils/fq2psmcfa -q20 diploid.fq.gz > diploid.psmcfa utils/splitfa diploid.psmcfa > split.psmcfa psmc -N25 -t15 -r5 -p "4+252+4+6" -o diploid.psmc diploid.psmcfa seq 100 | xargs -i echo psmc -N25 -t15 -r5 -b -p "4+252+4+6" \ -o round-{}.psmc split.fa | sh cat diploid.psmc round-*.psmc > combined.psmc utils/psmc_plot.pl -pY50000 combined combined.psmc

If anybody could share their code or point out where I've gone wrong I'd appreciate it! Thank you.

bootstrap psmc • 2.1k views
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Heys, did you solve it? I'm exactly in the same situation as you, I don't understand if I'm doing something wrong or the code is outdated.

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The README file made a small mistake. It should be 'split.psmcfa' but not 'split.fa' in the command line. Just use the split.psmcfa file made by your former command line using the utils\splitfa. Like this

seq 100 | xargs -i echo psmc -N25 -t15 -r5 -b -p "4+25*2+4+6" \
    -o round-{}.psmc split.psmcfa | sh

But not this

seq 100 | xargs -i echo psmc -N25 -t15 -r5 -b -p "4+25*2+4+6" \
        -o round-{}.psmc split.fa | sh
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yes, agreed!

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