Hellow every one I used Two TF to do ChIP in Mouse tissues , ,I know usually we used unpaired end seq for ChIP but I used pair end seq. when i got the results, did mapping using Bowtie2 I got these strange results for mapping
7908233 reads: off these: 7908233 (100%) were paired; of these: 5096777 (64.45%) aligned concordantly 0 times 2186477 (27.65%) aligned concordantly exactly 1 time 624979 (7.90%) aligned concordantly >1 times ...... 5096777 pairs aligned concordantly times: of these: 1284864 (25.21%) aligned disconcordantly 1 time ......... 3811913 pairs aligned 0 times concordanlty or disconcordantly 7623826 mates make up the pairs; of these: 6918974 (90.75%) aligned 0 times 262375 (3.44 %) aligned exactly 1 time 442477 (5.80%) aligned >1 times 56.25% overall alignment rate
I know that >70% unique mapping is normal but i could not understand these results what they explain and is it good mapping or not ? my seq resulty according to mapping is good or not
Peaks: Another thing is the Peak number when i find theh peaks number is very low like 244 for IgG and 222 for TF1 and 170 for TF2 and when i filter them against igG it goes further lower number my first question according to this situtaion is i think usually the peak number for TF across the genome is in thousands but its in hundards? second IgG seams to have higher peak number then the samples ?