Question: problem with uploading wiggle files to UCSC
0
gravatar for ashkan
3.2 years ago by
ashkan110
ashkan110 wrote:

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 • 1.0k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by ashkan110

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

ADD REPLYlink written 3.2 years ago by genomax76k

yes. that is the genome I used for the alignment

ADD REPLYlink written 3.2 years ago by ashkan110
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