Error in uploading custom track

[Anandh Kumar]

Dear Sir/Madam,

I am trying to upload my bedgraph file to the UCSC custom track, it shows the error

" needMem: trying to allocate 963415552 bytes (limit: 500000000) "

When I compress the file as test.gz and trying to upload it says " Error File 'test.bedGraph.gz' - Error line 35955601 of somefile.gz: chromEnd larger than chrom chrM size (16572 > 16571)"

Can you suggest me some idea to solve the issue I am new to this bioinformatics.

Thanks and regards,

Kumar.

Anandhakumar Chandran

Department of Chemistry, Graduate School of Science, 

Kyoto University

Kitashirakawa-Oiwakecho, Sakyo-Ku Kyoto 606-8502, JAPAN

Phone +81-8047613634

[Brian Lee]

Dear Kumar,

Thank you for using the UCSC Genome Browser and your question about a bedgraph memory issue when uploading a file.

Please see this recent conversation: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/Eybt7oo8m5A/dhdFwDB8uMEJ

What would be best is to create a binary file that you can host on the internet that the browser can access so that only bits of the file are transferred when browsed, instead of the entire file.

For an overview you might want to look at this helpful wikipage: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format

What you would do is get the bedGraphToBigWig utility for your system. You can do uname -a and pick the utility from the matching directory here:http://hgdownload.soe.ucsc.edu/admin/exe/

Then you would get the chrom.sizes file for the matching assembly, in this case hg19 it appears. You can obtain it here:http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes

Then you could run a command like:
bedGraphToBigWig test.bedGraph hg19.chrom.sizes out.test.bw

If you there are some annotations that extend past the end of chromosomes, so you can avoid that problem using the -clip option, to clip these final entries.

Our engineer shares that the chrM message you see could be a symptom of how our hg19 assembly has a non-standard chrM, and that you might want to strip those entries out, you could that by cat test.bedGraph | grep -v "chrM" > test.edit.bedGraph. If you have more questions abou the chrM coordinates please feel free to reply with more questions.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead togenom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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