String of short sequences as a genome for Miseq reporter

vl80 · 03-13-2013, 10:31 PM

We did some PCR sequencing on Miseq and are trying to see if we could use a stringed together sequence of all amplicons to creat a pseudogenome and input for Miseq reporter in the resequencing option. As we have some internal barcodes in the products, each of our amplicons would have replicates with the different tags at each end. Anyone else has done something similar?

kcchan · 03-14-2013, 02:51 PM

It should work in theory, but I don't know if the inline barcodes will mess anything up in MSR.You can just try it and report back the results. All you have to do is upload a FASTA file in MCS, then use assign your samples to use it as the genome in MSR. You can requeue the analysis as many times as you want until you get things working just right.

vl80 · 03-21-2013, 04:57 PM

It does work! Now the next step would be to see if an annotation file can be created for the pseudo genome so that the Miseq reporter can put out the results with annotation. The annotation would be the identity. Could anyone shed some light on how to annotate a psedogenome...

kcchan · 03-21-2013, 06:12 PM

Is the fasta header not informative enough? You could also make a bed file that contains the identity information.

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03-13-2013, 10:31 PM	#1
vl80 Member Location: Asia Join Date: Nov 2012 Posts: 34	String of short sequences as a genome for Miseq reporter We did some PCR sequencing on Miseq and are trying to see if we could use a stringed together sequence of all amplicons to creat a pseudogenome and input for Miseq reporter in the resequencing option. As we have some internal barcodes in the products, each of our amplicons would have replicates with the different tags at each end. Anyone else has done something similar?

03-14-2013, 02:51 PM	#2
kcchan Senior Member Location: USA Join Date: Jul 2012 Posts: 184	It should work in theory, but I don't know if the inline barcodes will mess anything up in MSR.You can just try it and report back the results. All you have to do is upload a FASTA file in MCS, then use assign your samples to use it as the genome in MSR. You can requeue the analysis as many times as you want until you get things working just right.

03-21-2013, 04:57 PM	#3
vl80 Member Location: Asia Join Date: Nov 2012 Posts: 34	It does work! Now the next step would be to see if an annotation file can be created for the pseudo genome so that the Miseq reporter can put out the results with annotation. The annotation would be the identity. Could anyone shed some light on how to annotate a psedogenome...

03-21-2013, 06:12 PM	#4
kcchan Senior Member Location: USA Join Date: Jul 2012 Posts: 184	Is the fasta header not informative enough? You could also make a bed file that contains the identity information.