These are the list of files

Contol_Input_sorted.bam_rem.bam  
Control_H2BUb_sorted.bam_rem.bam  
Control_IgG_sorted.bam_rem.bam 
PTPN6_g2_6_H2Bub_sorted.bam_rem.bam  
PTPN6_g2_6_Input_sorted.bam_rem.bam

So to get unique files i do this

 ls -1 *bam | sort | sed -r 's/_sorted.bam_rem.bam//g' | sort | uniq 
Contol_Input
Control_H2BUb
Control_IgG
PTPN6_g2_6_H2Bub
PTPN6_g2_6_Input

Now i have to run each sample against input and IgG for peak-calling. Like Control_H2BUb_sorted.bam_rem.bam against

Contol_Input_sorted.bam_rem.bam & Control_IgG_sorted.bam_rem.bam and 


PTPN6_g2_6_H2Bub_sorted.bam_rem.bam against PTPN6_g2_6_Input_sorted.bam_rem.bam

So how do I parse and execute using gnu parallel.

I came across this tutorial where it does something like this

cat sample_names.txt | parallel --max-procs=12 'macs2 callpeak -t {}-A-NC.sorted.bam \
 -c {}-G-NC.sorted.bam -g hs -n {}-A-NC-sharp-model -q 0.01 --outdir {}-A-NC-sharp-model-peaks 2> {}-A-NC-sharp-model.stderr'

Now im not sure how to pass the file names as argument for IP and Input or IgG.

If i use logic a little bit i have to fix Control and PTPN6_g2_6 as constant naming!.

Any suggestion or help would be really appreciated.

These are the list of files

Control_Input_sorted.bam_rem.bam  
Control_H2BUb_sorted.bam_rem.bam  
Control_IgG_sorted.bam_rem.bam 
PTPN6_g2_6_H2Bub_sorted.bam_rem.bam  
PTPN6_g2_6_Input_sorted.bam_rem.bam

So to get unique files i do this

 ls -1 *bam | sort | sed -r 's/_sorted.bam_rem.bam//g' | sort | uniq 
Control_Input
Control_H2BUb
Control_IgG
PTPN6_g2_6_H2Bub
PTPN6_g2_6_Input

Now i have to run each sample against input and IgG for peak-calling. Like Control_H2BUb_sorted.bam_rem.bam against

Contol_Input_sorted.bam_rem.bam & Control_IgG_sorted.bam_rem.bam and 


PTPN6_g2_6_H2Bub_sorted.bam_rem.bam against PTPN6_g2_6_Input_sorted.bam_rem.bam

So how do I parse and execute using gnu parallel.

I came across this tutorial where it does something like this

cat sample_names.txt | parallel --max-procs=12 'macs2 callpeak -t {}-A-NC.sorted.bam \
 -c {}-G-NC.sorted.bam -g hs -n {}-A-NC-sharp-model -q 0.01 --outdir {}-A-NC-sharp-model-peaks 2> {}-A-NC-sharp-model.stderr'

Now im not sure how to pass the file names as argument for IP and Input or IgG.

If i use logic a little bit i have to fix Control and PTPN6_g2_6 as constant naming!.

Any suggestion or help would be really appreciated.