Hi Mali,
Thank for your question. You've helped us find a small bug in the
txBedToGraph program. The program is having issues with very small
records. One of our engineers will work on fixing this bug, but I am
uncertain of the time-frame. For now, please filter out the records with
less than 14 bases (only 5 records) and the program should be able to
complete without error. It finished for us after filtering these out
(bed12.txt is the file we created when we retrieved hg18 Ensembl data
from the table browser):
cat bed12.txt | gawk '{if (($3 - $2) >= 14) print $1 "\t" $2 "\t" $3}' >
bedmin14.txt
Please contact the mail list ([email protected]) again if you have any
further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
On Tue Nov 15 00:12:50 2011, mali salmon wrote:
>
> Dear Sir/Madam
> I have been trying to generate a table of alternative splicing events of
> ensembl human genes (hg18).
> I have downloaded a BED file of these genes from the table browser, and
> then tried to run txBedToGraph and I got the following error:
> "needLargeMem: trying to allocate 0 bytes (limit: 4294967297)"
> The input file was downloaded from your table browser so I suppose the
> format is correct.
> Any idea how to solve the problem?
> Thanks
> Mali
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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