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add backslash to target code #3

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -58,7 +58,7 @@ Each step is executed by a single command.
-l : optional, the length of flanking sequences (on the BLAST hit), default is 2000 bp.

**Example using the provided input data:**
`./find_overlapping_regions.sh -t Sample_input/Target_genomes -r Sample_input/Reference_genomes/ -o first_step_output/`
`./find_overlapping_regions.sh -t Sample_input/Target_genomes/ -r Sample_input/Reference_genomes/ -o first_step_output/`

#### b. Second command:
**From the folder in which the SynTracker scripts are located, execute:**
Expand Down Expand Up @@ -87,4 +87,4 @@ Changes to simplify and solve file naming procedure, and solve BLAST error resul
a. Added script "old_to_new_names.py": changes the file names in the target folder to "Sample.xxx", fasta headers to "contig.yyy", writes the changes to a table, and assigns all sequences to a single file. It is called from find_overlapping_regions.sh.
b. Modified "find_overlapping_regions.sh", to use "old_to_new_names.py" instead of sed command in step 1.
c. Modified "SynTracker.R" to read the table generated by "old_to_new_names.py" and change temporarily assigned sample names back to the original sample names (i.e., file names).
d. Changed "SynTracker_functions.R" to handle the new naming format.
d. Changed "SynTracker_functions.R" to handle the new naming format.