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Old 04-20-2016, 09:36 AM   #1
cacti
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Default Multiple files with same barcode in TCGA

Does anyone know what differentiates the bam files from samples with the same barcode? in TCGA For example, this sample (TCGA-D7-8575-01A-11D-2340-08) has files *.5.bam and *.1.bam. What is the difference?


C440.TCGA-D7-8575-01A-11D-2340-08.5.bam
C1646.TCGA-D7-8575-01A-11D-2340-08.1.bam
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Old 04-20-2016, 12:26 PM   #2
Richard Finney
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It's some kind of version number; they appear to be exclusively associated with "BI", broad institute.
It's not clear whether newer ones are replacing the previous version or if they are a separate run and are therefore additional information.
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Old 04-20-2016, 01:38 PM   #3
GenoMax
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Not an answer for your question but see this link: https://browser.cghub.ucsc.edu/searc...1A-11D-2340-08 If you scroll over to the right in the table you can see that there are 2 live files. If you click on the "i" symbol you can get additional information (choose "show details in new window"). These may be two separate runs for the sample looking at the submission date.
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Old 04-21-2016, 02:38 PM   #4
m_two
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The same aliquot may have been sequenced multiple times and/or processed multiple times:

Some aliquots have been sequenced for VALIDATION, WGS, and WXS
Some aliquots have been captured with different probe sets.

Some data may have been aligned to NCBI36, GRCh37, and GRCh38.

Some data have had additional reads added or removed after the version used in a publication was generated so both versions are live.

You can query CGHub for these details:

library_type
assembly
published
uploaded
modified
state
reason
reagent_vendor
reagent_name

or pull them from columns 1,8,13,23-26,31-33 of the MANIFEST at

https://cghub.ucsc.edu/reports/SUMMA...T_MANIFEST.tsv
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