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Forum: Ion Torrent 01-14-2018, 06:17 PM
Replies: 37
Views: 39,384
Posted By HiroMishima
In our protocol, we performed AmpliSeq multiplex...

In our protocol, we performed AmpliSeq multiplex PCR using the following materials:
1) original AmpliSeq primers: containing target-specific sequences with uracil nucleobases but not containing...
Forum: Ion Torrent 01-09-2018, 04:22 PM
Replies: 37
Views: 39,384
Posted By HiroMishima
Thank you for your question. A1) We...

Thank you for your question.



A1) We did AmpliSeq primer cutting. For amplicons, we used uracil DNA glycosylase and endonuclease IV. This step obtained amplicons without primers outside...
Forum: Ion Torrent 12-31-2017, 02:31 AM
Replies: 37
Views: 39,384
Posted By HiroMishima
Hi all, In the following paper, we described...

Hi all,

In the following paper, we described a technique to prepare Illumina libraries using AmpliSeq amplicons:
J Hum Genet https://www.nature.com/articles/s10038-017-0392-9
PubMed...
Forum: Bioinformatics 05-22-2014, 08:14 PM
Replies: 29
Views: 15,794
Posted By HiroMishima
BINGO! GenoMax, I appreciate your informative...

BINGO! GenoMax, I appreciate your informative advices.

The followings are a protocol to prepare to use Bcl2Fastq on Ubuntu 14.04 LTE:

sudo alien -i bcl2fastq-1.8.4-Linux-x86_64.rpm
sudo...
Forum: Bioinformatics 05-22-2014, 06:06 PM
Replies: 29
Views: 15,794
Posted By HiroMishima
Ubuntu 13.10 : perl v5.14.2-21 Ubuntu...

Ubuntu 13.10 : perl v5.14.2-21
Ubuntu 14.04 LTS : perl v5.18.2-2

So far, I have used only system default perls.
Forum: Bioinformatics 05-22-2014, 04:48 PM
Replies: 29
Views: 15,794
Posted By HiroMishima
Thnak you GenoMax for asking me further...

Thnak you GenoMax for asking me further information.

Before installing bcl2fastq, I purged the package using "sudo dpkg --purge bcl2fastq" to uninstall completely. Errors were not reported during...
Forum: Bioinformatics 05-21-2014, 04:28 PM
Replies: 29
Views: 15,794
Posted By HiroMishima
Yes it is. I'm sorry for submitting without a...

Yes it is. I'm sorry for submitting without a quoting.

I installed bcl2fastq-1.8.4-Linux-x86_64.rpm using the alien command into Ubuntu 13.10. After upgrading Ubuntu to 14.04 LTS,...
Forum: Bioinformatics 05-21-2014, 10:39 AM
Replies: 29
Views: 15,794
Posted By HiroMishima
I have same problem. The rpm file worked on...

I have same problem. The rpm file worked on Ubuntu 13.10 using Perl v5.14.2-21, however, it does not work on Ubuntu 14.04 LTS using Perl v5.18.2-2. So far I cannot solve the problem.
Forum: SOLiD 10-31-2011, 06:05 PM
Replies: 12
Views: 3,681
Posted By HiroMishima
I had the same problem. According to the...

I had the same problem.

According to the LifeTech's support, the heartbeat timeout limit is set in the file "/share/apps/lifescope/etc/analysis/system.properties". Find a line,...
Forum: SOLiD 10-31-2011, 05:40 PM
Replies: 12
Views: 6,816
Posted By HiroMishima
Hi, Without using LifeTech's...

Hi,

Without using LifeTech's BioScope/LifeScope, I think the following pipeline can be applied to SOLiD data for SNP/indel detection.

1) *.csfasta+*.qual / *.XSQ -> SAM/BAM
BFAST, BWA, or...
Forum: SOLiD 06-30-2011, 09:43 PM
Replies: 16
Views: 5,882
Posted By HiroMishima
Our 5500 SOLiD and the LifeScope cluster were...

Our 5500 SOLiD and the LifeScope cluster were delivered this week and will be set up next week.

While I am waiting for machines, I am reading manuals of the cluster based on Scyld SclusterWare...
Forum: Bioinformatics 11-17-2010, 05:30 PM
Replies: 132
Views: 44,417
Posted By HiroMishima
Everything's perfect! cutadapt 0.5.1 worked well...

Everything's perfect! cutadapt 0.5.1 worked well with two -a options.

I believe that cutadapt is one of the best adopter sequence trimmer especially in term of simpleness and speed.

Thanks...
Forum: Bioinformatics 11-17-2010, 04:32 AM
Replies: 132
Views: 44,417
Posted By HiroMishima
I found that I used two -a options and used...

I found that I used two -a options and used adapter sequences were almost reverse complement each other. Probably I do not have to use two -a options in this case. Hopefully, these examples clarify...
Forum: Bioinformatics 11-16-2010, 08:16 PM
Replies: 132
Views: 44,417
Posted By HiroMishima
3'-end partial match of adapters

Hi,

I have a question about Cutadapt version 0.3.

Does Cutadapt cut partial sequences of adapters?

According to "Statistics for adapter" messages, Cutadapt seems to recognize 3'-end...
Forum: Introductions 08-31-2009, 12:02 AM
Replies: 373
Views: 101,206
Posted By HiroMishima
Smile Introduction from Japan

Hi all,

I am Hiro Mishima, and a research fellow at Department of Human Genetics, Nagasaki University, Nagasaki, Japan. I am working on a project of resequencing/sequence-capturing of human genome...
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