I am wondering if galaxy has tool to substring/extract sequence/text
from another sequence/text based on coordinates in columns (start, end
column) or how to do it in Text Manipulation/Compute?
all the best,
The tool "Fetch Sequences -> Extract Genomic DNA" can be used to
fasta sequences. The coordinates can be BED, GTF, etc. and the
doesn't necessarily have to be an actual genome, just a fasta file in
To subset a data string, the tool "Text Manipulation -> Trim" might be
helpful. This would only work if you want to use the same rules for an
entire file (or split your file up and run the tool on those subfiles
using different rules). Practical for some cases, but not all.
And the final option is for coordinate data - tools in "Operate on
Genomic Intervals". Once you have the final coordinate set, going back
and using the "Fetch Sequences" tool can capture the associated result
fasta sequence, from a native genome or a fasta file in your history,
Hopefully this gives you an option that will work for your project,