added example to workflow for bed file

docs/workflows.md

@@ -3,9 +3,19 @@
 ## Extract and re-basecall reads mapping to a particular genomic region
 
 ```sh
+# extract region chrX:147911919-147951125
 samtools view https://url/to/reads.bam chrX:147911919-147951125 | cut -f1  | sort -u > rid_list.txt
+
+# OR
+
+# extract regions from a BED file
+samtools view https://url/to/reads.bam -L /path/to/regions.bed -M | cut -f1 | sort -u > rid_list.txt
+
+# fetch reads corresponding to the extracted region
 slow5curl get https://url/to/reads.blow5 --list rid_list.txt -o extracted.blow5
-buttery-eel -i extracted.blow5  -g /path/to/ont-guppy/bin/ --config dna_r9.4.1_450bps_sup.cfg --device 'cuda:all' -o extracted_sup.fastq # see https://github.com/Psy-Fer/buttery-eel/ for butter-eel options
+
+# basecall extracted BLOW5, see https://github.com/Psy-Fer/buttery-eel/ for butter-eel options
+buttery-eel -i extracted.blow5  -g /path/to/ont-guppy/bin/ --config dna_r9.4.1_450bps_sup.cfg --device 'cuda:all' -o extracted_sup.fastq 
 ```
 
 Note: If the read IDs in the BAM file are not the parent IDs (happens when read splitting is enabled during the initial basecalling step), you can grab the parent read IDs from the FASTQ file as below and use that as the input the to slow5curl get.
@@ -16,8 +26,10 @@ The above assumes that `parent_read_id` tag is present in all reads including th
 ```sh
 # for split reads, get the parent_read_id tag
 grep -F -f rid_list.txt reads.fastq | sed -n -e 's/.*parent\_read\_id=//p' | awk '{print $1}' > tmp.txt
+
 # for non split reads, get the normla read ID
 grep -F -f rid_list.txt reads.fastq | grep -v "parent\_read\_id" | awk '{print $1}' | tr -d '@' >> tmp.txt
+
 # remove duplicates
 sort -u tmp.txt > parent_rid_list.txt
 ```