SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Do not use "adapter trimming" in MiSeq Reporter 2.0.25 ECO Illumina/Solexa 9 12-10-2013 04:38 AM
PC Requirements for MiSeq Reporter and others softwares zgtmann Bioinformatics 5 03-21-2013 06:21 AM
Miseq reporter demultiplexing sunleaf Illumina/Solexa 6 03-11-2013 12:52 PM
Downsample data for MiSeq Reporter kmcarr Illumina/Solexa 7 01-29-2013 04:16 AM
generate CIGAR string from 2 sequences? bbimber Bioinformatics 0 03-20-2010 09:44 AM

Reply
 
Thread Tools
Old 03-13-2013, 09:31 PM   #1
vl80
Member
 
Location: Asia

Join Date: Nov 2012
Posts: 34
Default 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?
vl80 is offline   Reply With Quote
Old 03-14-2013, 01:51 PM   #2
kcchan
Senior Member
 
Location: USA

Join Date: Jul 2012
Posts: 184
Default

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.
kcchan is offline   Reply With Quote
Old 03-21-2013, 03:57 PM   #3
vl80
Member
 
Location: Asia

Join Date: Nov 2012
Posts: 34
Default

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...
vl80 is offline   Reply With Quote
Old 03-21-2013, 05:12 PM   #4
kcchan
Senior Member
 
Location: USA

Join Date: Jul 2012
Posts: 184
Default

Is the fasta header not informative enough? You could also make a bed file that contains the identity information.
kcchan is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:24 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO