I am new to bedtools. I have an alignment file from bowtie2: op.sam. In order to convert it to bed, I did the following
samtools view -bSq 25 -h -F 260 op.sam | samtools sort - -o sorted_read.bam
samtools index sorted_read.bam
bedtools bamtobed -i sorted_read.bam > sorted_read.bed
The sorted bed file looks like
chr1 6811028 6811203 M00181:330:000000000-ANP8N:1:1106:13069:9454_TTATGCTAAGTATC 44 -
chr1 6811028 6811203 M00181:330:000000000-ANP8N:1:1108:14515:6525_TTATGCTAAGTATC 44 -
chr1 6811028 6811203 M00181:330:000000000-ANP8N:1:1114:27695:8423_TTATGCTAAGTATC 44 -
The first 4 columns are chr,start,end and read id and the last column is strand. I don't understand what the 5th column represents? The bed format says that it is score, but I don't know what it represents. Please help me understand this. thanks
