bwtool matrix error - invalid signed integer

Question

[rbronste]

Hi all,

I am using bwtool to make a matrix for footprinting a TF using a BED file I generated with meme and some bigwig files from my data:

bwtool matrix 200:200 /sonas-hs/args/hpc_norepl/home/rbronste/FoxA1_fimo.bed /sonas-hs/args/hpc_norepl/home/rbronste/FastQ_data/p14_033016/cutadapt_75bp/bigWigs_mm10/296834SamtoolsRmDup.bigWig /sonas-hs/args/hpc_norepl/home/rbronste/FoxA1output.txt

Error: invalid signed integer: "53.4"

I see a column in the bed file corresponding to the strand with two different integers for +/- and can't figure out why I am getting this error. Anyone have any clue? Thanks!

Rob

[Pierre Lindenbaum]

what is the output of

grep -F '53.4'  /sonas-hs/args/hpc_norepl/home/rbronste/FoxA1_fimo.bed

[rbronste]

chr1    3061763 3061773 1-1205-chr1 53.4    +   fimo    nucleotide_motif    .   Name=1;ID=1-1205-chr1;pvalue=4.55e-06;qvalue= 0.741;sequence=AAAGTAAACA;

Answer 1

[Pierre Lindenbaum]

If bwtool expects a standard BED ( https://genome.ucsc.edu/FAQ/FAQformat#format1), the column 4 should be an integer (53) , NOT a floating number (53.4)

[rbronste]

That did the trick thanks!