bed from bowtie2 aligner

Question

[zizigolu]

Hi,

I have a bed file resulted from using bowtie2 of which I pasted few rows in the below, may someone please tell me what the columns 4 and 5 are?

YAL002W    245    268    SRR2046309.48055214    42    +
YAL002W    2043    2066    SRR2046309.8820148    42    +
YAL003W    6    34    SRR2046309.28608934    42    +
YAL003W    27    52    SRR2046309.47255981    42    +
YAL003W    30    55    SRR2046309.13168252    42    +
YAL003W    32    52    SRR2046309.16880912    42    +

Thank you

[Devon Ryan]

It looks like the score is the MAPQ. There's no predefined way that BAM files should be converted to BED format, so technically anything other than the first 3 columns can mean pretty much anything. Odds are that entries are just alignments, which would explain why column 4 contains read names from an SRA dataset.

[zizigolu]

thank you, sorry you mean I bed file I don't need columns 4, 5 and 6 necessarily??? and the first 3 columns will suffice?

Answer 1

[Antonio R. Franco]

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

42 is a value, normally ranged between 0 and 1000, that indicates how strongly has the gene representation be drawn in the browser

+ and - means the watson or the crick strand of the DNA, that is, if the representation of the genes goes forward or reverse

[zizigolu]

thank you very much