ValueError: invalid literal for int() with base 10: 'start' computeMatrix of deeptools
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4.1 years ago
salamandra ▴ 410

When running the command with deeptools:

DIR=~/TESTING/day2_fos20_intersection
computeMatrix scale-regions -S path/HDF_day20.bw \
path/HUVEC_day2.bw \
-R $DIR/day2_fos20.bed $DIR/day2.bed $DIR/fos20.bed -b 4000 -a 4000 --regionBodyLength 5000 --missingDataAsZero -bs 50 -out HDFd20vsHUVd2_matrixscale.gz

I get the error:

ValueError: invalid literal for int() with base 10: 'start'

What am I doing wrong?

ChIP-Seq Deeptools • 3.3k views
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0
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No header. I have some Chr17_gl00205_random though...don't know if that is a problem

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Please post the first 10 or so lines of your BED files.

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I have to ask you sorry. you were so right!

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No worries!

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4.1 years ago
venu 6.8k

Does your bed files have a header? If yes, try removing and run it again.

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They don't have headers, I checked ;)

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Are you sure? By header I meant chr start end. I added this header to my bed file and used the command you mentioned. It is exactly giving the same error

ValueError: invalid literal for int() with base 10: 'start'

Without header it works completely fine.

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2.9 years ago
udi.landau ▴ 30

In my case I had NA`s in the bed file

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