diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md
index e87bdb8..c19be85 100644
--- a/PhyloToL-Part-1:-GF-assignment.md
+++ b/PhyloToL-Part-1:-GF-assignment.md
@@ -71,9 +71,11 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai
 Role of each script
 <img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%">
 
+* **Main inputs** : The main inputs for processing transcriptomes are: a folder containing the assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (this must be current version of the hook)), and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts).
+* **Outputs** : The main outputs after processing transcriptomes are: ReadyToGo files which contain the nucleotide and amino acid sequences of each taxa, and a summary information of the sequences processed for each taxa.
 
-To run the PhyloToL part 1 for processing transcriptomes, run:
-* `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases > log.txt`
+####To run the PhyloToL part 1 for processing transcriptomes, run:
+ `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases > log.txt`
 
 Available parameters are:
 | Parameter | Type| Options| Description|
@@ -90,11 +92,11 @@ Available parameters are:
 | --maxlen  |int|-| Maximum transcript length | 
 | --seq_count  |int|-| minimum number of sequences after assigning OGs | 
 
-
 To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run: 
 `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases --xplate_contam --conspecific_names Conspecific.txt > log.txt`
 
 
+
 ### Processing genomes
 Role of each script
 <img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Genomes_scripts.png" width="100%">
@@ -112,8 +114,7 @@ Role of each script
 | --databases| str| Path to databases folder | The folder should contain all 3 databases|
 
 
-* **Main inputs** : A folder containing the assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData), a folder containing the Databases, and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts).
-* **Outputs** : ReadyToGo files (AA and NTD) and taxon summary.
+
 * *Optional inputs : Gcodes.txt and Conspecific.txt
 * *The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates.
 * _Example:_