How to unmask a soft masker genome?

Question

[Diego]

Hi all,

I wonder if you know a good way to unmask a soft masked genome (i.e., atatata --> ATATATA).

Thanks in advance

[barslmn]

You can try tr command

tr '[:lower:]' '[:upper:]'

[Istvan Albert]

in all fairness this would alter the sequence names as well, usually that is not a desired behavior

[barslmn]

Yes you need to skip the names some way.

while read -r line; do case "$line" in ">"*) echo "$line";; *) echo $(echo $line | tr '[:lower:]' '[:upper:]');; esac;done < myref.fa

Answer 1

[Istvan Albert]

You can use a tool like seqkit

https://bioinf.shenwei.me/seqkit/usage/

seqkit seq 

 -u, --upper-case                print sequences in upper case

Answer 2

[GenoMax]

Using reformat.sh from BBMap suite

reformat.sh -Xmx2g in=masked.fa out=unmasked.fa tuc=t