pages*: add missing mnemonics (#12151)

* pages*: add missing mnemonics

---------

Co-authored-by: Sebastiaan Speck <12570668+sebastiaanspeck@users.noreply.github.com>
Co-authored-by: Lena <126529524+acuteenvy@users.noreply.github.com>
Co-authored-by: K.B.Dharun Krishna <kbdharunkrishna@gmail.com>

pages/common/bedtools.md

@@ -4,26 +4,26 @@
 > Used to intersect, group, convert and count data in BAM, BED, GFF/GTF, VCF format.
 > More information: <https://bedtools.readthedocs.io>.
 
-- Intersect two files regarding the sequences' strand and save the result to the specified file:
+- Intersect file [a] and file(s) [b] regarding the sequences' [s]trand and save the result to a specific file:
 
-`bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -s > {{path/to/output_file}}`
+`bedtools intersect -a {{path/to/file_A}} -b {{path/to/file_B1 path/to/file_B2 ...}} -s > {{path/to/output_file}}`
 
-- Intersect two files with a left outer join, i.e. report each feature from `file1` and NULL if no overlap with `file2`:
+- Intersect two files with a [l]eft [o]uter [j]oin, i.e. report each feature from `file1` and NULL if no overlap with `file2`:
 
-`bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -lof > {{path/to/output_file}}`
+`bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -loj > {{path/to/output_file}}`
 
 - Using more efficient algorithm to intersect two pre-sorted files:
 
 `bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -sorted > {{path/to/output_file}}`
 
-- Group file `path/to/file` based on the first three and the fifth column and summarize the sixth column by summing it up:
+- [g]roup a file based on the first three and the fifth [c]olumn and apply the sum [o]peration on the sixth column:
 
 `bedtools groupby -i {{path/to/file}} -c 1-3,5 -g 6 -o sum`
 
-- Convert bam-formatted file to a bed-formatted one:
+- Convert bam-formatted [i]nput file to a bed-formatted one:
 
 `bedtools bamtobed -i {{path/to/file.bam}} > {{path/to/file.bed}}`
 
-- Find for all features in `file1.bed` the closest one in `file2.bed` and write their distance in an extra column (input files must be sorted):
+- Find for all features in `file1.bed` the closest one in `file2.bed` and write their [d]istance in an extra column (input files must be sorted):
 
 `bedtools closest -a {{path/to/file1.bed}} -b {{path/to/file2.bed}} -d`