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Forum: RNA Sequencing 01-26-2011, 04:00 PM
Replies: 29
Views: 13,254
Posted By zukey
Is SAM format output file avaliable now?

Hmmsplicer got non-canonical junctions from illumina RNA-seq single reads successfully. Now I need to get expression levels for all transcripts. I thought about cufflinks, which requires mapped reads...
Forum: RNA Sequencing 10-21-2010, 07:02 AM
Replies: 29
Views: 13,254
Posted By zukey
I am trying the HMMSplicer. Could anyone let me...

I am trying the HMMSplicer. Could anyone let me know how to load paired-end data (illumina) to it?

Thanks alot,

Qi
Forum: Bioinformatics 10-13-2010, 08:12 AM
Replies: 9
Views: 2,378
Posted By zukey
Could you send me the link to short reads or part...

Could you send me the link to short reads or part of them? I will give a try.

Thanks,

Qi
Forum: Illumina/Solexa 10-13-2010, 07:28 AM
Replies: 3
Views: 2,234
Posted By zukey
We had a very similar case here. RTA stopped in...

We had a very similar case here. RTA stopped in Read1. But RTA1.8 did get intensities from images and certainly deleted images. We finished Read2. Then, we just use OLB convert the intensities to...
Forum: Bioinformatics 10-13-2010, 07:13 AM
Replies: 9
Views: 2,378
Posted By zukey
Our internal software may help....

Length of your sequences? Which sequencing platform, illumina or 454?
We have a internal-built program ACGT101 to analysis the miRNAs including filtering tRNAs from RFam database. If you need our...
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