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Old 12-14-2011, 11:59 AM   #1
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Location: Alabama, US

Join Date: Dec 2011
Posts: 5
Default Rescuing mate-pair data

Hello all,

We recently had trouble with the sequencing facility we use and got a bad batch of genomic runs back that I would like to attempt to “rescue” and assemble. The runs should have been mate-paired reads of 100 bases with a 3kb insert on an Illumina sequencer (one whole lane/sample). However, there was a problem when the data was taken off the machine and one set of reads is incomplete. The one set (e.g. right) of reads came off alright (100 bases of high quality each), but the other reads (e.g. left) were cut short ~45 bases (each read has 55 high quality bases followed by 45 Ns). So we basically have reads of 100 bases mate-paired with reads of only 55 bases and a 3kb insert.

Any suggestions on possible ways to rescue these genomic runs?

Thanks in advance for any suggestion,
weeseda is offline   Reply With Quote
Old 12-14-2011, 12:36 PM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

55 bases should be enough to align correctly, so I think it should still work out alright.
swbarnes2 is offline   Reply With Quote

assemble, genomics, illumina, mate-paired reads, research solution

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