deeptools computeMatrix error

Question

[EagleEye]

Hello,

I am facing some problem using deeptools (deeptools 2.4.2). Someone please help me solving this issue.

Command:

computeMatrix scale-regions -S ./H3K4me2_sorted_nodup.bigWig -R genes.bed --beforeRegionStartLength 2000  --skipZeros -o ./H3K4me2_sorted_nodup_matrix.mat.gz

Input (header):

track type=wiggle_0 name="H3K4me2" description="H3K4me2_sorted_nodup"
variableStep chrom=chr1
56375   3
56385   3
564493  3
564503  5
564513  5
564523  4
564533  4
564543  6

Error:

[bwHdrRead] There was an error while reading in the header!
Traceback (most recent call last):
  File "/usr/local/bin/computeMatrix", line 11, in <module>
    main(args)
  File "/usr/local/lib/python2.7/dist-packages/deeptools/computeMatrix.py", line 414, in main
    hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
  File "/usr/local/lib/python2.7/dist-packages/deeptools/heatmapper.py", line 235, in computeMatrix
    chromSizes, _ = getScorePerBigWigBin.getChromSizes(score_file_list)
  File "/usr/local/lib/python2.7/dist-packages/deeptools/getScorePerBigWigBin.py", line 161, in getChromSizes
    fh = pyBigWig.open(fname)
RuntimeError: Received an error during file opening!

Answer 1

[Devon Ryan]

That's a wiggle file, not a bigWig file. You'll need to convert it.

[EagleEye]

Yes, sorry. It is working perfectly. Thanks for the tool (saves lot of time).