Question: ValueError: invalid literal for int() with base 10: 'start' computeMatrix of deeptools
0
gravatar for salamandra
3.4 years ago by
salamandra330
salamandra330 wrote:

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 • 2.9k views
ADD COMMENTlink modified 2.2 years ago by _r_am31k • written 3.4 years ago by salamandra330

No header. I have some Chr17_gl00205_random though...don't know if that is a problem

ADD REPLYlink written 3.4 years ago by salamandra330

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

ADD REPLYlink written 3.4 years ago by Devon Ryan97k
1

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

ADD REPLYlink written 3.4 years ago by salamandra330

No worries!

ADD REPLYlink written 3.4 years ago by Devon Ryan97k
2
gravatar for venu
3.4 years ago by
venu6.7k
Germany
venu6.7k wrote:

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

ADD COMMENTlink written 3.4 years ago by venu6.7k

They don't have headers, I checked ;)

ADD REPLYlink written 3.4 years ago by salamandra330

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.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by venu6.7k
0
gravatar for udi.landau
2.2 years ago by
udi.landau20
udi.landau20 wrote:

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

ADD COMMENTlink written 2.2 years ago by udi.landau20
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