Partial-runs.md

 You may not want to use the entire workflow of MOSCA. Here follow some interesting examples of tasks that are better executed running parts of MOSCA separately. The following commands assume you have installed MOSCA [as instructed](https://github.com/iquasere/MOSCA/wiki/Installing-and-running-MOSCA).
 
-## Preprocess NGS reads
+# Preprocess NGS reads
 
 MOSCA's preprocessing script can be used standalone, as it automatically downloads all resources required.
 ```
 python ~/anaconda3/envs/mosca/share/MOSCA/scripts/preprocess.py -i {your input reads (e.g. mg_R1.fq,mg_R2.fq)} -t {number of threads} -o {output directory} -adaptdir {resources directory}/adapters -rrnadbs {resources directory}/rRNA_databases -d {data_type (either "dna" or "mrna")} -rd {resources directory} -n --minlen {minimum length of reads to keep} --avgqual {minimum average quality of reads to keep}
-```
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+```
+
+# Run MOSCA without replicates
+
+MOSCA's differential expression analysis module requires replicates. MOSCA's analysis is still possible without replicates by bypassing this task:
+1. First, preprocess your datasets as explained [above](https://github.com/iquasere/MOSCA/wiki/Partial-runs#Preprocess-NGS-reads)
+2. Join your reads by sample by running, for each "forward" and "reverse" files, the following command:
+```
+cat {forward_file} >> {output}/Preprocess/{sample}_forward.fastq
+cat {reverse_file} >> {output}/Preprocess/{sample}_forward.fastq
+```
+3. Perform assembly by running this, for each sample
+```
+python ~/anaconda3/envs/mosca/share/MOSCA/scripts/assembly.py -r {output}/Preprocess/{sample}_forward.fastq,{output}/Preprocess/{sample}_reverse.fastq -t {threads} -o {output}/Assembly/{sample} -a {assembler (either "metaspades" or "megahit"} -m {max_memory}
+```
+4. Perform binning, if you want to, by running, for each sample
+```
+python ~/anaconda3/envs/mosca/share/MOSCA/scripts/binning.py -c {output}/Assembly/{sample}/contigs.fasta -t {threads} -o {output}/Binning/{sample} -r {output}/Preprocess/{sample}_forward.fastq,{output}/Preprocess/{sample}_reverse.fastq -mset {markerset (either "107" or "40")}
+```
+5. Perform gene calling and annotation over the contigs by running, for each sample
+```
+python ~/anaconda3/envs/mosca/share/MOSCA/scripts/annotation.py -i {output}/Assembly/{sample}/contigs.fasta -t {threads} -o {output}/Annotation/{sample} -em {error_model} -db {path/to/diamond_database.(fasta/dmnd)} -mts {diamond_max_target_seqs} --assembled"
+```
+6. Run UPIMAPI for each sample
+```
+upimapi.py -i {output}/Annotation/{sample}/aligned.blast -o {output}/Annotation/uniprotinfo --blast --full-id
+```
+7. 
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