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bwtool matrix error - invalid signed integer

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

bwtool matrix software error
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updated by Biostar Biostar • written by rbronste rbronste

what is the output of

grep -F '53.4'  /sonas-hs/args/hpc_norepl/home/rbronste/FoxA1_fimo.bed
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written by Pierre Lindenbaum Pierre Lindenbaum 
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;
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by rbronste rbronste

1 answer

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)

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written by Pierre Lindenbaum Pierre Lindenbaum

That did the trick thanks!

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written by rbronste rbronste

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