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Search: Posts Made By: hi-koike
Forum: General 08-29-2014, 07:40 AM
Replies: 9
Views: 4,108
Posted By hi-koike
Hi Victoria, I am sorry to hear that you...

Hi Victoria,

I am sorry to hear that you could not run on centOS neither.

I am not sure the version of centOS which I used, because I am traveling
abroad. It might be CentOS 6 because I...
Forum: Bioinformatics 08-28-2014, 11:51 AM
Replies: 10
Views: 3,721
Posted By hi-koike
Hi blakeoft, Thank you. As you pointed, I...

Hi blakeoft,

Thank you. As you pointed, I will wait the answer for my email.

I tried to read the perl script, but the count was done by
a binary code "count". So I need a help from a well...
Forum: Bioinformatics 08-28-2014, 11:22 AM
Replies: 10
Views: 3,721
Posted By hi-koike
Hi dpryan, Thank you for your advice....

Hi dpryan,

Thank you for your advice. Actually I did, but it didn't work.
I would appreciate any idea.

Thank you,
Hideaki
Forum: Bioinformatics 08-28-2014, 09:37 AM
Replies: 10
Views: 3,721
Posted By hi-koike
Negative RPKM values by EDGE-pro

Hello,

I am using your EDGE-pro programs for RNA-seq analysis
of bacterial species.
I could run the program, but I got negative values for some of
the samples.

I found rRNA.numberReads was...
Forum: General 08-20-2014, 06:27 AM
Replies: 9
Views: 4,108
Posted By hi-koike
Hi Victoria, Can you run a glimmer using...

Hi Victoria,

Can you run a glimmer using already trained files?
If you can, it might be the same problem I experienced.

Can you get a computer to run Cent OS or RedHat OS ?

I used an old...
Forum: General 08-19-2014, 08:08 AM
Replies: 9
Views: 4,108
Posted By hi-koike
Lightbulb Hi Victoria, What Linux OS did you use? I...

Hi Victoria,

What Linux OS did you use?
I tried to run training on Ubuntu OS, but I failed.:(
Then I tried to run on Cent OS and it worked.:)

I am not sure the reason, but anyway I could...
Forum: General 05-15-2014, 03:33 AM
Replies: 9
Views: 4,108
Posted By hi-koike
Question I would like to know if anyone have solved the...

I would like to know if anyone have solved the problem ?

Thanks in advance,
Hideaki
Forum: Illumina/Solexa 09-02-2013, 01:10 PM
Replies: 5
Views: 4,186
Posted By hi-koike
Hi winsettz, We are assembling a fungus...

Hi winsettz,

We are assembling a fungus which might have a genome size around 20 Mbp and
having more than 25 chromosomes.
We have a reference genome of a different strain which has been...
Forum: Illumina/Solexa 09-02-2013, 10:51 AM
Replies: 5
Views: 4,186
Posted By hi-koike
Hi Luc, No we did not. Because the amount of...

Hi Luc,

No we did not. Because the amount of the obtained DNA were low and just enough for the recommended amount for Library construction, we decided not to do any enrichment for specific...
Forum: Illumina/Solexa 08-31-2013, 04:33 PM
Replies: 5
Views: 4,186
Posted By hi-koike
Question de novo assembling using NEBNext™ dsDNA Fragmentase™

Hello all,

I'd like to know if anyone has tried de novo assembling from a library made by gDNA fragmentation NEBNext™ dsDNA Fragmentase™.

What software(s) are good for the de novo assembling of...
Forum: Bioinformatics 07-23-2013, 09:16 AM
Replies: 2
Views: 1,830
Posted By hi-koike
Hello Jamie, Thank you for your reply. The...

Hello Jamie,

Thank you for your reply. The thread is helpful for my understanding.
Your blog is also helpful and interesting to read.

Thanks,
Hideaki
Forum: Bioinformatics 07-22-2013, 08:03 AM
Replies: 2
Views: 1,830
Posted By hi-koike
Question overlapping in PE library sequencing

Hello,

I'd like to do de novo assembling of a fungal genome(~20 Mbp).
I will use Miseq data for the assembling.

I found some programs can handle overlapping sequence of the two
paired end...
Forum: De novo discovery 07-18-2013, 07:56 AM
Replies: 0
Views: 1,886
Posted By hi-koike
Question Miseq v2 PE library length for Allpaths-LG

Hello,

I'd like to use ALLPATHS-LG for de novo assembling of a fungal genome
(~20 Mbp). I will use Miseq data for the assembling.

I am wondering the length of fragment for paired read can be...
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