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Question about the Table browser
31-Mar-2014, 07:47 AM
Post: #1
Question about the Table browser
Hello,

I am using your GWIPS database for translation efficiency analyses.


1) I have noticed that when I try to download ribosome profiling data for the entire genome, an arbitrary position appears suddenly. For example: for s.cerevisiae (track: Brar 2012, table A14201) in the 'region' Table browser control I select 'genome' but the following specific 'position' shows up: 'chrXV:784,600-792,400'.
It happens for all organisms...

2) I am using the data from all available in your database for large scale analyses. I had a problem with S.cerevisiae data, I have re-download it today and I wonder whether you have updated the data recently (it seems that each chromosome has the same number of reads (1024)..).


Your response would be greatly appreciated.

Many thanks for the database!

Best Regards,
Renana

it doesn't contain only 1024 reads.. however it is separated into sections:

#bedGraph section chrI:338-8254
#bedGraph section chrI:8259-24858

*Based on what are the sections separated?
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31-Mar-2014, 07:56 AM
Post: #2
RE: Question about the Table browser
Hi,

In reply to the first query, the position that will appear in the Table Browser is the chromosomal position that was being viewed in the Genome Browser. However, when "genome" is selected, the output will be for the genome and not the chromosome position. The position field can also be cleared.

In response to the second query, if the filter option is not set, then the output will be broken into chromosome sections starting with commented out entries "#bedGraph section ...".

If you don't want "#bedGraph section ..." lines in your output, then create a filter size (the 1,000,000,000 option should cater for all datasets).

Hope this explains your output format and thanks for your query.
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