formatting

README.md

@@ -52,16 +52,16 @@ Optional:
 
 
 ## Output
-Expected: A non-redundant TE library: $genome.EDTA.TElib.fa. The curated library is included in this file if provided.
+Expected: A non-redundant TE library: $genome.mod.EDTA.TElib.fa. The curated library is included in this file if provided.
 
 Optional:
-1. Novel TE families: $genome.EDTA.TElib.novel.fa. This file contains TE sequences that are not included in the curated library (`--curatedlib` required).
-2. Whole-genome TE annotation: $genome.EDTA.TEanno.gff. This file contains both structurally intact and fragmented TE annotations (`--anno 1` required).
-3. Summary of whole-genome TE annotation: $genome.EDTA.TEanno.sum (`--anno 1` required).
-4. Low-threshold TE masking: $genome.MAKER.masked. This is a genome file with only long TEs (>=1 kb) being masked. You may use this for de novo gene annotations. Annotated gene models should contain TEs and need further filtering (`--anno 1` required).
-5. Annotation inconsistency for simple TEs; $genome.EDTA.TE.fa.stat.redun.sum (`--evaluate 1` required).
-6. Annotation inconsistency for nested TEs: $genome.EDTA.TE.fa.stat.nested.sum (`--evaluate 1` required).
-7. Oveall annotation inconsistency: $genome.EDTA.TE.fa.stat.all.sum (`--evaluate 1` required).
+1. Novel TE families: $genome.mod.EDTA.TElib.novel.fa. This file contains TE sequences that are not included in the curated library (`--curatedlib` required).
+2. Whole-genome TE annotation: $genome.mod.EDTA.TEanno.gff. This file contains both structurally intact and fragmented TE annotations (`--anno 1` required).
+3. Summary of whole-genome TE annotation: $genome.mod.EDTA.TEanno.sum (`--anno 1` required).
+4. Low-threshold TE masking: $genome.mod.MAKER.masked. This is a genome file with only long TEs (>=1 kb) being masked. You may use this for de novo gene annotations. Annotated gene models should contain TEs and need further filtering (`--anno 1` required).
+5. Annotation inconsistency for simple TEs; $genome.mod.EDTA.TE.fa.stat.redun.sum (`--evaluate 1` required).
+6. Annotation inconsistency for nested TEs: $genome.mod.EDTA.TE.fa.stat.nested.sum (`--evaluate 1` required).
+7. Oveall annotation inconsistency: $genome.mod.EDTA.TE.fa.stat.all.sum (`--evaluate 1` required).
 
 
 ## EDTA Usage (regular installation)
@@ -97,7 +97,7 @@ Activate the EDTA program:
 ### Divide and conquer
 *Identify intact elements of a paticular TE type*:
 
-1. Get raw libraries from a genome (specify `-type ltr|tir|helitron` in different runs)
+1.Get raw libraries from a genome (specify `-type ltr|tir|helitron` in different runs)
 
     perl EDTA_raw.pl [options]
       --genome	[File]	The genome FASTA