Question: Command for counting gene model after each round of MAKER
0
gravatar for Elizabeth
17 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 • 357 views
ADD COMMENTlink modified 17 months ago by ringourquia20 • written 17 months ago by Elizabeth20

What does summary.sh ?

ADD REPLYlink written 17 months ago by Juke344.6k
1
gravatar for ringourquia
17 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 17 months ago by ringourquia20
1

Thank you. It works.

ADD REPLYlink written 17 months ago by Elizabeth20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1256 users visited in the last hour