Hello,
I am trying to align my data with reference genome using Bowtie2. But I need to change the read start, as I read in "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position":
For peak-calling and footprinting, we adjusted the read start sites to represent the center of the transposon binding event. Previous descriptions of the Tn5 transposase show that the trans-poson binds as a dimer and inserts two adaptors separated by 9 bp (ref. 11). Therefore, all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the – strand were offset −5 bp.
Anyone knows how can I do it?
Thanks.
I am trying to align my data with reference genome using Bowtie2. But I need to change the read start, as I read in "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position":
For peak-calling and footprinting, we adjusted the read start sites to represent the center of the transposon binding event. Previous descriptions of the Tn5 transposase show that the trans-poson binds as a dimer and inserts two adaptors separated by 9 bp (ref. 11). Therefore, all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the – strand were offset −5 bp.
Anyone knows how can I do it?
Thanks.