Hi, I have the 8 bed files footprints_1.bed, footprints_2.bed (sorted, and work well with other bedtools commander), like
chrY 59017131 59017352 MAZ 99.9928 -
chrY 59017132 59017353 MAZ 99.9989 -
chrY 59017132 59017353 VEZF1 99.9671 -
chrY 59017133 59017354 ZN467 99.9616 -
chrY 59017134 59017355 MAZ 99.9603 -
chrY 59017134 59017355 ZN467 99.7886 -
chrY 59017135 59017356 MAZ 99.9841 -
chrY 59017135 59017356 VEZF1 99.9903 -
chrY 59017140 59017352 MZF1 99.9998 -
chrY 59017141 59017362 VEZF1 99.9993 -
when I convert them to bigbed,
./binarycommander/bedToBigBed footprints_1.bed http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes footprints_1.bb
I did not get footprints.bb; however, information is shown
footprints_1.bed
end (2) before start (1999786) line 2665221 of footprints_1.bed
footprints_2.bed
end (2) before start (1999786) line 2551396 of footprints_2.bed
footprints_3.bed
end (7) before start (699779) line 1608375 of footprints_3.bed
---
What does the information mean? Could anyone help me solve the issues? Thank you.
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written
by
zhaolin20042008 •
the message is quite clear, you have some start values greater than the end value.
you can display those lines using:
awk 'int($2)>int($3)' *.bed
Thank you. I checked the line 2551396 of footprints_2.bed
chr2 1999786 2e+06 ELF5 99.9799 +
So change awk 'BEGIN {OFS="\t"} {print $1,int($2),int($3), $4}' footprints_2.bed |sort -k1,1 -k2,2n > new.footprints_2.bed
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