hello every one,
I have paired end illumina reads, R1.fastq and R2.fastq and I have mapped them as single-end reads by using bowtie2 default parameters, I performed further downstream analysis by using samtools and bedops, and now I have R1.bed and R2. bed I made two sets, one of them have R1_uniquely_mapped.bed, R2_uniquely_mapped.bed and second of them R1_mapped_more_than_1.bed , R2_mapped_more_than_1.bed.
because R1 and R2 belongs paired end reads, and my restriction library has maximum 2KB size, then R1 and R2 pairs must be present in less than 2 kb territory of chromosome
theoretically I am assuming, in R1.bed format,
chr1 100 180 @R1_read1______1 .................
chr1 1000 1090 @R1_read2______1................In R2.bed format,
chr1 2100 2180 @R2_read1_____2............. ## I just add 2KB length with respect to R1.bed###
chr1 2500 2590 @R2_read______2......... ## I just add 1.5KB [1500nts] with respect to R1.bed, because my library is >= 2KB.How can I customize downstream tools like BEDOPS or bedtool which can capture such type of reads or alignment????? How can I filter this type of infromation by using bedops tool????
all suggestions and comments are most welcome,