Interpreting bed file...
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6.6 years ago
ab.tsubaki ▴ 50

Hi there

I hope someone can help me out here. I have a bed file that I obtained from a bamfile and I am struggling to interpret what the columns mean. The pipeline I followed was as follows: From my gff file I used getfastabed and the output was aligned using bowtie to paired end fastq files. The subsequent bam file was converted to bed and my data of that file looks like this:

gene 0 92 MG00HS16:756:HYLC3ADXX:1:1109:6409:61076/1 0 +

Can anyone help me out or point me in the right direction? Especially interpreting the 4th column. I have not been able to find something similar via Google.

Thanks in advance

bedfile bamfile gff • 2.2k views
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ucsc provides definition for format like bed and bigBed definition are available here : https://genome.ucsc.edu/FAQ/FAQformat.html

In your case I don't understand your bed. usually a bed is chromosome start end and optional column. Hope the link I provided may help you.

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6.6 years ago
michael.ante ★ 3.7k

Hi,

you may first look your fasta reference you created. There might be spaces in the fasta header, which might be included in the alignment (samtools view -H ) but might not be carried over to the bed-file.

Your 4th column is a read name. Meaning, you converted each alignment of the bam-file into bed-format. Alternatively, you can use genomeCoverageBed to produce a coverage-profile.

Cheers,

Michael

[Edit: Typo]

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