Open tan5251 opened 3 years ago
It is the results of normal samples. Parsing ChIP file(s): ./bedpe/d331Ip.bedpe Total eligible paired end reads: 12015516
Valid ChIP reads: 11661132 (12015516 before out of bounds removal)
Score threshold: 18.686
Number of tags in a window: 3
Number of islands found: 33710
Parsing Input file(s): ./bedpe/d331In.bedpe Total eligible paired end reads: 12467232
Valid Background reads: 12438786 (12467232 before out of bounds removal)
Found a median fragment size of 321.5
Using chromosome sizes found in ../Genomes/genome.fa/chrsome_len_1.txt.
This is the results of "abnormal" samples. Parsing ChIP file(s): ./bedpe/d332Ip.bedpe Total eligible paired end reads: 15613622
Valid ChIP reads: 15115491 (15613622 before out of bounds removal)
Score threshold: 25.125
Number of islands found: 32601
Parsing Input file(s): ./bedpe/d332In.bedpe Total eligible paired end reads: 14749377
Valid Background reads: 14727361 (14749377 before out of bounds removal)
Found a median fragment size of 1212731.0
Using an effective genome length of ~2432 * 1e6
I actually do not know. I did not implement the paired end processing :/
The fragment size is based on the 100 first lines in your files IIRC. Before any removal of potentially bad fragments.
My data is 150PE. But the median framgent size in some samples is bigger to 100000. It really confuse me. Is it normal and why it happen ?
It is the results of normal samples. Parsing ChIP file(s): ./bedpe/d331Ip.bedpe Total eligible paired end reads: 12015516
Valid ChIP reads: 11661132 (12015516 before out of bounds removal)
Score threshold: 18.686
Number of tags in a window: 3
Number of islands found: 33710
Parsing Input file(s): ./bedpe/d331In.bedpe Total eligible paired end reads: 12467232
Valid Background reads: 12438786 (12467232 before out of bounds removal)
Found a median fragment size of 321.5
Using chromosome sizes found in ../Genomes/genome.fa/chrsome_len_1.txt.
Using an effective genome length of ~2432 * 1e6
This is the results of "abnormal" samples. Parsing ChIP file(s): ./bedpe/d332Ip.bedpe Total eligible paired end reads: 15613622
Valid ChIP reads: 15115491 (15613622 before out of bounds removal)
Score threshold: 25.125
Number of tags in a window: 3
Number of islands found: 32601
Parsing Input file(s): ./bedpe/d332In.bedpe Total eligible paired end reads: 14749377
Valid Background reads: 14727361 (14749377 before out of bounds removal)
Found a median fragment size of 1212731.0
Using chromosome sizes found in ../Genomes/genome.fa/chrsome_len_1.txt.
Using an effective genome length of ~2432 * 1e6