Hi, I am trying to identify repeat regions in the reference sequence and masked using Mummer. I tried the following command at Mummer. However, it gives the regions in a text file. Please let me know how to get the fasta file after masking the repeats so I can use these masked fasta file for Smalt software.
Hi, I am trying to identify repeat regions in the reference sequence and masked using Mummer. I tried the following command at Mummer. However, it gives the regions in a text file. Please let me know how to get the fasta file after masking the repeats so I can use these masked fasta file for Smalt software.
repeat-match ref_seq.fasta > ref_seq.repeats
Output file::
Start1 Start2 Length
906850 1399638r 72
184976 1399638r 72
351538 1399638r 72