Question: Command for counting gene model after each round of MAKER
0
gravatar for Elizabeth
6 months ago by
Elizabeth20
Elizabeth20 wrote:

Hello, I am looking for a command that can tell me the number of gene models after each round of MAKER. I have tried the following:

less Maker2.all.gff |awk '$3=="mRNA"' |grep "mRNA-1" |awk '{print $5-$4}' |summary.sh

cat <roundN.full.gff> | awk '{ if ($3 == "gene") print $0 }' | awk '{ sum += ($5 - $4) } END { print NR, sum / NR }'

But, my terminal seems to hang, every time I run the command. Has anyone encountered a similar problem ?

gene model maker count • 175 views
ADD COMMENTlink modified 6 months ago by ringourquia20 • written 6 months ago by Elizabeth20

What does summary.sh ?

ADD REPLYlink written 6 months ago by Juke-342.9k
1
gravatar for ringourquia
6 months ago by
ringourquia20
ringourquia20 wrote:

The "fathom -gene-stats" command used in the path to generate the SNAP learning-file displays several stats of your gff including the number of genes. Otherwise, I use:

cut -f3 your_merged_gff.gff | grep "gene" | wc -l
ADD COMMENTlink written 6 months ago by ringourquia20
1

Thank you. It works.

ADD REPLYlink written 6 months ago by Elizabeth20
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