Question: understanding bamtobed output
0
gravatar for sumithrasank75
4.7 years ago by
United States
sumithrasank75140 wrote:

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

alignment • 3.3k views
ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 4.7 years ago by sumithrasank75140
0
gravatar for ben.kunfang
3.2 years ago by
ben.kunfang30
ben.kunfang30 wrote:

I think its represent to MAPQ score, see detail in this thread:How to interpret the outputs generated from bamtobed using BedTools?

ADD COMMENTlink written 3.2 years ago by ben.kunfang30
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