Question: Negative start position bed file
0
gravatar for chariko
4.4 years ago by
chariko30
Spain
chariko30 wrote:

I aligned two samples  (bwa; filter with samtools, removed duplicates with picard-tools, bamtobed and bed to bedgraph with genomeCoverageBed) to a genome file consisting in 4 genes and the first sample went fine but the second one when getting the bed file the start position for one of the genes was -1. I wonder that is not correct but I do not know why did I obtain such negative value.

Example:

"Wrong bed file for gene1"
gene1      -1      150      M00...      37         -
gene1      -1          150      M01...      37         +
gene2      1004      1115      M00...      60         -

I realized that -1 values in special cases, however, BEDPE (bed paired end) positions may be set to -1 to indicate that one or more ends of a BEDPE feature is unaligned.

[url]http://bedtools.readthedocs.org/en/latest/content/overview.html[/url]

but I do not understand if that´s my case and I really do not understand why did it align if it was unaligned....

Any clues?

start bed file negative • 1.2k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by chariko30

Looks like an off by one error.

ADD REPLYlink written 4.4 years ago by Devon Ryan88k

thanks for your answer, but... what do you mean off by one error? 

would you consider to discard this result and that´s all?

thanks again

ADD REPLYlink written 4.4 years ago by chariko30
1

Have a look at the wikipedia article, this is a pretty common type of program bug. You can probably just convert the -1 values to 0.

ADD REPLYlink written 4.4 years ago by Devon Ryan88k
1

ok but if the zeros are off by one isn't it likely that the other rows are off by one as well  ;-) ?

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Istvan Albert ♦♦ 79k

Indeed :)        

ADD REPLYlink written 4.4 years ago by Devon Ryan88k

cann't say, why its negative

may be you can  just convert -1 to +1

ADD REPLYlink written 4.4 years ago by Manvendra Singh2.0k
1
gravatar for chariko
4.4 years ago by
chariko30
Spain
chariko30 wrote:

Afeter changing the data to 0 and 1, I decided to remove those reads because also the coverage was very low (3x) so I really do not belive the results.

Thanks all for your answers.

ADD COMMENTlink written 4.4 years ago by chariko30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1983 users visited in the last hour