Is it necessary to execute command (samtools sort -n) before run Deduplication?

[changchuanjun]

@FelixKrueger, hello! Thanks for your excellent work on the Bismark, this software facilitates community to study DNA methylation.
I have finished Alignment step with the command:

for i in $(cat sample.txt)
do
~/software/Bismark/bismark
--bowtie2
-X 1000
--score_min L,0,-0.6
--genome_folder /lns
-1 ./${i}_1_val_1.fq.gz
-2 ./${i}_2_val_2.fq.gz
--output_dir ./${i}_bismark_bowtie2_p1_X1000score_min_L_0_0.6_20240204
1>./${i}_bowtie2_X1000score_min_L_0_0.6.log 2>&1
done

and got a BAM output like this

Next step is Deduplication.
Now I have a question is it necessary to execute command (samtools sort -n) before run Deduplication?
or can I execute the Deduplication command(deduplicate_bismark mybamfile.bam) directly?
I am looking forward to your reply sincerely.

[FelixKrueger]

You can run the deduplication directly, files are written out with R1 and R2 directly following each other. Good luck!

[changchuanjun]

Thanks! I get it.