Hi I am trying to exclude a span of nucleotides from inbetween my contigs. I have the contig IDs and the start:end position as given below. I would like to remove all the bases between start & end.
> ID length start..end >Contig1 100 20..35 > Contig2 30 3..12
If contig1 looks like below, I want to exclude the bases in bold by splitting the sequence and then create a new sequence with the bases on either side of the excluded region.
Most of the tools that i encountered remove the bases from trailing ends. Please let me know if you have any suggestions to specify the start:end and create a new sequence excluding that region.
I have about 100 contigs to clean this way. Any help would be highly appreciated. Thank you so much!