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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,
David
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,
David
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