Added output info

docs/options/alignment.md

@@ -286,3 +286,28 @@ For reads that have multiple alignments a random alignment is written out to a s
 - `--rfg <int1>,<int2>`
 
   Sets the reference gap open (&lt;int1>) and extend (&lt;int2>) penalties. A reference gap of length N gets a penalty of `<int1> + N * <int2>`. Default: 5, 3.
+
+
+#### OUTPUT:
+
+The output is a BAM format by default, as well as a aligment report deduplication report (ending in '_deduplication_report.txt')
+
+For a single-end file called 'simulated.fastq', the expected output for Bowtie 2, HISAT2 or minimap2 is:
+
+```
+simulated_bismark_bt2.bam
+simulated_bismark_bt2_SE_report.txt
+simulated_bismark_hisat2.bam
+simulated_bismark_hisat2_SE_report.txt
+simulated_bismark_mm2.bam
+simulated_bismark_mm2_SE_report.txt
+```
+
+In a paired-end situation, for files 'simulated_1.fastq' and 'simulated_2.fastq' you would expect for Bowtie2 or HISAT2:
+
+```
+simulated_1_bismark_bt2_pe.bam
+simulated_1_bismark_bt2_PE_report.txt
+simulated_1_bismark_hisat2_pe.bam
+simulated_1_bismark_hisat2_PE_report.txt
+```

docs/options/deduplication.md

@@ -4,7 +4,7 @@ This script is supposed to remove alignments to the same position in the genome
 
 !!! important
 
-    Please note that for paired-end BAM files the deduplication script expects Read1 and Read2 to follow each other in consecutive lines! If the file has been sorted by position make sure that you resort it by read name first (e.g. using samtools sort -n)
+    Please note that for paired-end BAM files the deduplication script expects Read1 and Read2 to follow each other in consecutive lines! If the file has been sorted by position make sure that you resort it by read name first (e.g. using `samtools sort -n`)
 
 A brief description of the Bismark deduplication and a full list of options can also be viewed by typing `deduplicate_bismark --help`.
 
@@ -60,7 +60,7 @@ The path to your Samtools installation, e.g. `/home/user/samtools/`. Does not ne
 Print version information and exit
 
 
-#### OUTPUT
+#### OUTPUT:
 
 The output is a BAM format by default, as well as a deduplication report (ending in '_deduplication_report.txt')