These are the list of files
Contol_Input_sortedControl_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_InputControl_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.