Question: Command for counting gene model after each round of MAKER
0
gravatar for Elizabeth
5 weeks 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 • 93 views
ADD COMMENTlink modified 5 weeks ago by ringourquia10 • written 5 weeks ago by Elizabeth20

What does summary.sh ?

ADD REPLYlink written 5 weeks ago by Juke-342.2k
1
gravatar for ringourquia
5 weeks ago by
ringourquia10
ringourquia10 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 5 weeks ago by ringourquia10
1

Thank you. It works.

ADD REPLYlink written 5 weeks 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: 767 users visited in the last hour