What is the difference between rmdup_sam and rmdup_sam2 files?

[chatterjee89]

Hi Dr. Cao,

I had some questions regarding the duplicate removal steps. With the following code, I understand that we are removing duplicates based on identical UMI, tagmentation site, reverse transcription index and ligation adaptor index...

`echo "Start removing duplicates..."
echo input folder: $filtered_sam_folder
echo output folder: $rmdup_sam_folder
mkdir -p $rmdup_sam_folder
module unload python

bash_script=$script_path/sci3_rmdup_nomismatch.sh
Rscript $R_script $bash_script $filtered_sam_folder $sample_ID $rmdup_sam_folder $core $mismatch

echo
echo "Start removing duplicates..."
echo input folder: $all_output_folder/rmdup_sam
echo output folder: $all_output_folder/rmdup_sam_2
mkdir -p $all_output_folder/rmdup_sam_2
module unload python

bash_script=$script_path/sci3_rmdup_nomismatch.sh
filtered_sam_folder=$all_output_folder/rmdup_sam
rmdup_sam_folder=$all_output_folder/rmdup_sam_2
Rscript $R_script $bash_script $filtered_sam_folder $sample_ID $rmdup_sam_folder $core $mismatch`

My questions are:
1. What exactly is the difference between the sam files in rmdup_sam and rmdup_sam_2 folders?
2. Why are two rounds of the same script being run post barcode attachment?
3. The previous step is barcode+UMI attachment but the way I read it, we are only attaching the barcode, does that sound right? I don't understand where the UMI is being defined. Am I missing something?

I am trying to understand which step is doing exactly what within sci3_main.sh and hence the questions.
Thank you!

Regards,
Deep