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.
http://bedtools.readthedocs.org/en/latest/content/overview.html
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?
1 answer
Log in to answer this question.
-
bedGraph for Coverage of Insert from Paired-End Data?
written by RelativeOptics •
-
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
written by cheesefish21 •
-
Duplicate chromosome location columns in a bed file makes problem in importing them into R
written by minoo •
-
All vs All blast not self hit? Orthogroup clustering and single copy genome?
written by Charly •
-
Why the bed file not recognized as a bed file
written by brgs •
-
BED score in bedpe file: even though I filtered out by -q 255, why score 1 exists in resulting .bed…
written by Gene42 •
-
MACS2 produces different results using BAMPE and BEDPE
written by Marius •
-
Filtering paired and single end reads from a BAM file
written by James Ashmore
-
Which Of The Genes Are Enriched With Repeat Elements
written by roll
-
How To Get Annotation For Bed File From Another Bed File
written by k.nirmalraman
Looks like an off by one error.
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
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.
ok but if the zeros are off by one isn't it likely that the other rows are off by one as well ;-)?
Indeed :)
Can't say, why its negative
Maybe you can just convert -1 to +1