Hallo everyone,
I work at the University of Amsterdam and we have recently done a 454 Titanium run on normalized cDNA from tomato tissue. I have used the software from Roche- GS De Novo Assembler, to align the reads (non-paired) from the ssf files. I was wondering if anyone has used the software and can answer some questions about the output files:
1) I have noticed that (within an isogroup) sometimes the sequence of an isotig doesn't match with the contig sequences- so the contigs (and reads) all align but the corresponding isotig has a totally different sequence
2) Also I see in some isotigs that reads are being added (towards the 3') that don't have any overlapping sequence with the reads before
If someone has noticed these things with the data they are analyzing, I would appreciate any comments!
Thank you,
Eleni
I work at the University of Amsterdam and we have recently done a 454 Titanium run on normalized cDNA from tomato tissue. I have used the software from Roche- GS De Novo Assembler, to align the reads (non-paired) from the ssf files. I was wondering if anyone has used the software and can answer some questions about the output files:
1) I have noticed that (within an isogroup) sometimes the sequence of an isotig doesn't match with the contig sequences- so the contigs (and reads) all align but the corresponding isotig has a totally different sequence
2) Also I see in some isotigs that reads are being added (towards the 3') that don't have any overlapping sequence with the reads before
If someone has noticed these things with the data they are analyzing, I would appreciate any comments!
Thank you,
Eleni
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