Some problem about 454 gs flx+

[lcl283946181]

hello!
I have a problem about GS FLX+(the latest instrument).
1. we recovery the capture beads which have enriched DNA a few days ago, melt solation(NaOH) went into microcentrifuge tube (with capture beads, enriched DNA) on MPC, then there are any capture beads in supernatant?
2. I use GS De novo assembler to Splice a set of MiSeq datas(1X150), it was aborted when several hour, and some errors appear in the display. can i use GS De novo assembler to analyse illumina datas?

Thank you ahead of time,
liuchunlei

[pmiguel]

hello!
I have a problem about GS FLX+(the latest instrument).
1. we recovery the capture beads which have enriched DNA a few days ago, melt solation(NaOH) went into microcentrifuge tube (with capture beads, enriched DNA) on MPC, then there are any capture beads in supernatant?

Not sure I follow you here. Maybe you could post more details. Especially when you did each step, how much time elapsed between steps and what you want to know.

2. I use GS De novo assembler to Splice a set of MiSeq datas(1X150), it was aborted when several hour, and some errors appear in the display. can i use GS De novo assembler to analyse illumina datas?

Thank you ahead of time,
liuchunlei

In principle, the newest version of gsAssembler (2.6) should be able to assemble data in fastq format. So it should be possible, however there may be issues with the volume of data given it. Perhaps you could try to assemble 10% of the MiSeq data set?

--
Phillip

[lcl283946181]

Not sure I follow you here. Maybe you could post more details. Especially when you did each step, how much time elapsed between steps and what you want to know.

In principle, the newest version of gsAssembler (2.6) should be able to assemble data in fastq format. So it should be possible, however there may be issues with the volume of data given it. Perhaps you could try to assemble 10% of the MiSeq data set?

--
Phillip

hello！
Phillip，my version of gsAssembler is v2.6, is the newest. it is able to assemble data in fastq/fasta format. some in roche of china also recommended to reduce the amount of data, but i didn't get a chance to try, i think this is right answer,thank you!

[tokikake]

hello!
I have a problem about GS FLX+(the latest instrument).
1. we recovery the capture beads which have enriched DNA a few days ago, melt solation(NaOH) went into microcentrifuge tube (with capture beads, enriched DNA) on MPC, then there are any capture beads in supernatant?
liuchunlei

Hi,

did you check, if after the second melting Step the white DNA beads still cluster at the enrichment beads on the MPC?
If that is the case I would suggest to decrease the copies per bead number, because it seems that there is to much DNA in your emPCR and even after melting they clustered with the erichment beads.
At least, that is what happened to me last week.