diff --git a/README.md b/README.md
index 9a476fbd5e42bc3a440e48bbd27ae32c957b880a..3dcc2e52217c8d6ebfbfcd8e92a60ae83bd148bd 100644
--- a/README.md
+++ b/README.md
@@ -11,12 +11,13 @@ Inputs to the simuation:
 1. Csv-formatted table “GeneID,Counts” specifying the number of transcripts expressed, on average, for each gene in a given cell type. These can come for example from a bulk RNA-seq experiment of sorted cells of a given type. 
 2. File with the genome sequence
 3. gff/gtf-formatted file with the transcript annotation of the genome
-4. Number of reads to sequence
-5. Number of cells to simulate
-6. Mean and standard deviation of RNA fragment length
-7. Read length 
-8. Probability of intron inclusion - considered constant per intron to start with, can be extended to intron-specific. In the latter case, estimates could be obtained from bulk RNA-seq data by dividing the average per-position coverage in a given intron by the average per-position coverage of the gene, or of flanking exons.
-9. Option to add poly(A) tails to transcripts and an associated function for generating these tails (with specific length distribution and non-A nucleotide frequency).
-10. Parameters for evaluating internal priming: primer sequence, function implementing the constraints on priming sites (accessibility, energy of interaction, perfect matching at last primer position etc.).
+4. Output directory
+5. Number of reads to sequence
+6. Number of cells to simulate
+7. Mean and standard deviation of RNA fragment length
+8. Read length 
+9. Probability of intron inclusion - considered constant per intron to start with, can be extended to intron-specific. In the latter case, estimates could be obtained from bulk RNA-seq data by dividing the average per-position coverage in a given intron by the average per-position coverage of the gene, or of flanking exons.
+10. Option to add poly(A) tails to transcripts and an associated function for generating these tails (with specific length distribution and non-A nucleotide frequency).
+11. Parameters for evaluating internal priming: primer sequence, function implementing the constraints on priming sites (accessibility, energy of interaction, perfect matching at last primer position etc.).