I want to perform mapping in two ways.
One way is to run bowtie2 with my mouse data in the reference of mm10 and in this case everything works correct.
The other way of mapping is to map my data in a library of fragments created by Basic4Cseq functions. My firstCutter = "AAGCTT" and secondCutter ="GATC", then i transformed this csv to fasta file and i used it normally to build the index of bowtie2 and run bowtie2 mapping . The result of this mapping is extremely low. i tried to use different parameters but always i have very low rate of mapping results.
This is what i used for bowtie2 :
bowtie2 -q -x Library_fragments_Mouse --no-unal --score-min L,0,-0.25 -U iPSC_Pcdhb19_1_filtered.fastq -S iPSC_Pcdhb19_1_fragments_n.sam
The overall alignment rate is not more tha 13-15%.
Do you have any idea what could be the reason for this ? What kind of parameters should i use to have higher mapping rates ?