Hello everyone,
Since the arrival of TopHat2 I completely abandoned the use of TopHat1. The problem is that the "Wiggles" tool of TopHat does not exist for TopHat2. (In addition, the Wiggles tool was very slow). So I use IGVtools count, now, to generate my wig files. The problem is that the wig files are displayed in the IGV tool but not in the UCSC genome browser. Yet I have no error when uploading wig files in UCSC. But the data does not appear, the frame corresponding to the file remains empty. I can not find solutions to my problem.
Wig file I use :
track type=wiggle_0 name="sample_name" description="description" visibility=full alwaysZero=on windowingFunction=maximum
variableStep chrom=chr1 span=10
14371 1.8
14381 2
14391 2
14401 2
14411 1.8
14891 1
14901 1.6
14911 3.7
14921 5.1
14931 5.8
14941 5
14951 4.4
...
...
...
variableStep chrom=chr10 span=10
96331 1
96341 1
96351 1
96361 1
97191 1
97201 1
97211 1.5
97221 2
97231 2
97241 1
97251 1
97341 2
97351 2.9
...
...
...
Someone used IGVtools to generate these wig files? You encounter this problem?
And if not, what tool you used to generate wig file for RNA-seq data?
Thank you in advance for your help.
Since the arrival of TopHat2 I completely abandoned the use of TopHat1. The problem is that the "Wiggles" tool of TopHat does not exist for TopHat2. (In addition, the Wiggles tool was very slow). So I use IGVtools count, now, to generate my wig files. The problem is that the wig files are displayed in the IGV tool but not in the UCSC genome browser. Yet I have no error when uploading wig files in UCSC. But the data does not appear, the frame corresponding to the file remains empty. I can not find solutions to my problem.
Wig file I use :
track type=wiggle_0 name="sample_name" description="description" visibility=full alwaysZero=on windowingFunction=maximum
variableStep chrom=chr1 span=10
14371 1.8
14381 2
14391 2
14401 2
14411 1.8
14891 1
14901 1.6
14911 3.7
14921 5.1
14931 5.8
14941 5
14951 4.4
...
...
...
variableStep chrom=chr10 span=10
96331 1
96341 1
96351 1
96361 1
97191 1
97201 1
97211 1.5
97221 2
97231 2
97241 1
97251 1
97341 2
97351 2.9
...
...
...
And if not, what tool you used to generate wig file for RNA-seq data?
Thank you in advance for your help.
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