iCount xlsites--many reads with second-start not falling on segmentation

[ryanmarina]

I am attempting to determine cross-linking site with mapped reads, but certain libraries seem to give the same warning about several second starts not falling along segmentation borders when no custom segmentation file is provided (default):

Detecting cross-links...
All records in BAM file: 310737
Reads not mapped: 0
Mapped reads records (hits): 310737
Hits ignored because of low MAPQ: 0
Records used for quantification: 310737
Records with invalid randomer info in header: 310737
Records with no randomer info: 0
Ten most frequent randomers:
: 310737
There are 175499 reads with second-start not falling on segmentation. They are reported in file: /home/rmarina/scratch/iclip_data_download/beds/iCLIP_TDP-43_Brain_High_mm_beds/iCLIP_TDP-43_Brain_High_mm_skipped.bam
Saved to BED file (uniquely mapped reads): /home/rmarina/scratch/iclip_data_download/beds/iCLIP_TDP-43_Brain_High_mm_beds/iCLIP_TDP-43_Brain_High_mm_unique.bed
Saved to BED file (multi-mapped reads): /home/rmarina/scratch/iclip_data_download/beds/iCLIP_TDP-43_Brain_High_mm_beds/iCLIP_TDP-43_Brain_High_mm_multiple.bed

Can you explain what this means with no segmentation file provided, and if providing a custom segmentation reference will help recover some of these reads?