Question: understanding bamtobed output
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
gravatar for ben.kunfang
3.2 years ago by
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1813 users visited in the last hour