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.