problem with uploading wiggle files to UCSC
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5.0 years ago
ashkan ▴ 130

Hi Guys, I have made an script to build wiggle file from bam file (to upload them on UCSC genome browser). so far we have worked on human data and my script worked perfectly (I have made UCSC links for human data). our last experiment has been done on mouse and we got RNA-seq data from mouse. I did the same as what I have done using human data. also before uploading wiggle files I changed the browser to "mouse GRCm38/mm10". also I tried "mouse NCBI37/mm9".

but I got this error in both cases:

    Error File '4202.wig' - track load error (track name='ct_4202515110_4142'):
Couldn't find size of chromosome 1 (note: chrom names are case sensitive)

do you guys know how to resolve this problem?

genome • 1.5k views
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Did you align against a genome obtained from UCSC? Looks like there is a chromosome name mismatch in your file and UCSC.

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yes. that is the genome I used for the alignment

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