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Forum: De novo discovery 09-21-2012, 02:31 AM
Replies: 15
Views: 5,292
Posted By rururara
Definitely yes. Is there any concern about that?...

Definitely yes. Is there any concern about that? Do u mind to share? Anyway, I would like to try this approach whereby I assemble the parental reads with scaffold and use it as a reference sequence...
Forum: De novo discovery 09-21-2012, 02:11 AM
Replies: 15
Views: 5,292
Posted By rururara
Hi Zam & fcr, Yup, we are not in the same...

Hi Zam & fcr,

Yup, we are not in the same team. Hehe. Papaya is diploid. I have 3 samples and one of the sample is parental lines. I'm not sure yet the depth coverage as I am still not getting any...
Forum: De novo discovery 09-21-2012, 01:35 AM
Replies: 15
Views: 5,292
Posted By rururara
De novo SNP calling in absence of complete reference assembly

Hai all,

What about if the incomplete reference genome like papaya? The available information on papaya are scaffolds and contigs. Is it possible to use papaya scaffolds as a reference to align...
Forum: Bioinformatics 04-01-2012, 12:04 AM
Replies: 1
Views: 1,420
Posted By rururara
Bioinformatician in genotyping lab

Hai everyone,

I would like to share a few ideas and experiences with u guys who have been a bioinformatician who worked closely with molecular biologist in genotyping lab.

As I've been there,...
Forum: General 03-31-2012, 11:52 PM
Replies: 4
Views: 1,954
Posted By rururara
Bioinformatic services for labs

It would be better if the lab have at least one Bioinformatician. Yeah, it could be sufficient that people can outsource to the company for bioinformatic services especially in NGS data analysis. But...
Forum: Bioinformatics 03-25-2012, 06:22 PM
Replies: 7
Views: 4,949
Posted By rururara
hi qqtwee, i can't remember as it happen...

hi qqtwee,


i can't remember as it happen long time ago. but the key is u need to check whether u have the complete library that needed by Samtools to be succesfully installed.
try to read the...
Forum: De novo discovery 03-07-2012, 12:58 AM
Replies: 17
Views: 10,854
Posted By rururara
Dear all, Sorry if I'm asking a silly...

Dear all,

Sorry if I'm asking a silly sequence.
Can I clarify with u guys regarding GBS? Is that purposely done with DNA extraction? What about RNA extraction? Based on reading I found that for...
Forum: De novo discovery 03-06-2012, 11:17 PM
Replies: 17
Views: 10,854
Posted By rururara
Genotyping By Sequencing (GBS) and SNP calling

Thanks Zam,

I did also discuss with other researcher regarding this. Some of them prefer to write custom made script to call the SNP. but like me, i'm not really genius to write complicate script....
Forum: De novo discovery 03-06-2012, 04:34 AM
Replies: 17
Views: 10,854
Posted By rururara
Genotyping By Sequencing (GBS) and SNP calling

The idea to use Cortex for GBS is quite interesting. I thought utilized Velvet/Oases to assemble the genome would be the best way. I should consider and try Cortex tomorrow .

In my case , i work...
Forum: RNA Sequencing 03-06-2012, 04:12 AM
Replies: 6
Views: 6,048
Posted By rururara
RNA-seq SNP-calling without a complete reference

Hi all,

I tried also Oases for de novo transcriptome and quite satisfied with the output.
But now, I notice that how to obtain the SNP position from de novo assembly?
Can we just rely on the SNP...
Forum: Bioinformatics 12-07-2011, 11:06 PM
Replies: 0
Views: 2,078
Posted By rururara
MAQ-convert fasta to fastq

Hi all.

I have long sequences in fasta format and intend to convert it into fastq format.
The purpose is to discover the SNPs using bwa as alignment tool while SAMtools to call the SNPs.

Btw,...
Forum: Bioinformatics 04-19-2011, 06:56 PM
Replies: 48
Views: 62,184
Posted By rururara
hai all, i try to validate my snp in vcf...

hai all,

i try to validate my snp in vcf format using vcf-validator.
But it print out as below :


Expected GT as the first genotype field at Chr12:15841735
Expected GT as the first genotype...
Forum: Bioinformatics 04-17-2011, 08:28 PM
Replies: 0
Views: 1,586
Posted By rururara
est contigs as reference genome

Hai all,

Can est contigs becoma as a reference genome in mapping RNA seq?
For example, papaya draft is still in progress. Can I use that as a reference genome?
Or i should start with the de novo...
Forum: Bioinformatics 04-12-2011, 04:41 PM
Replies: 3
Views: 2,561
Posted By rururara
Hai nivea. Yup. I already solved the problem. I...

Hai nivea.
Yup. I already solved the problem. I dont think it's because of Java version.
It's depends on our BAM file. I tried to optimize back my alignment. Then I took out the uniquely mapping...
Forum: Bioinformatics 04-10-2011, 06:57 PM
Replies: 1
Views: 1,788
Posted By rururara
Analyse short reads using blast2go

Hi all,

Is it possible to analyse short reads in order to mining information?
For example, I would like to use blast2go to analyse my short reads but I'mnot sure the right approach. My idea is I...
Forum: Bioinformatics 04-07-2011, 10:44 PM
Replies: 1
Views: 4,977
Posted By rururara
convert blast output

hai all,

do you know how to convert blastall output into txt or gff format?

eg:

Query= OsSNP0002
(142 letters)

Database: ../u01/perl/uniprot-oryza-sativa-indica.fasta
Forum: Bioinformatics 03-31-2011, 06:47 AM
Replies: 0
Views: 2,665
Posted By rururara
vcftools to annotate SNP

Hi all.

I would like to know if u guys here experienced in SNP annotation using vcftools?
Well, I just want to get some ideas by using vcftools to associate the SNPs with related gene.
Is that...
Forum: Bioinformatics 03-22-2011, 06:03 PM
Replies: 1
Views: 2,538
Posted By rururara
mpileup and pileup results

Hi everyone.

1. I tried to call the snps using both mpileup and pileup.
There is more differences in snps calling numbers.
I found that mpileup give me less snps compared too pileup which...
Forum: Bioinformatics 03-21-2011, 01:52 AM
Replies: 7
Views: 4,949
Posted By rururara
thanks all. btw, success to install samtools. ...

thanks all.
btw, success to install samtools.
my mistaked because there is missing library.
i checked back the library and install.
then samtools is ok to use :)
Forum: Bioinformatics 03-21-2011, 12:26 AM
Replies: 7
Views: 4,949
Posted By rururara
i tried to upgrade the samtools 0.1.13 but still...

i tried to upgrade the samtools 0.1.13 but still couldnt find the mpileup.
i'm lost right now to install samtools eventhough i read the installation manual.
can u guys assist me on samtools...
Forum: Bioinformatics 03-17-2011, 11:38 PM
Replies: 7
Views: 4,949
Posted By rururara
unrecognized command mpileup

Hi,

I'm using samtools 0.1.7.
Suddenly I realized that 'mpileup' command is not recognized and when I checked back the mpileup command is not included in the samtools.
I run this cmd 'samtools...
Forum: Bioinformatics 03-08-2011, 11:20 PM
Replies: 8
Views: 4,958
Posted By rururara
I had this kind of problem too. I only can view...

I had this kind of problem too. I only can view my alignment and snps distributions in Artemis and Tablet. Why so hard to view in IGV :(
Forum: Bioinformatics 03-08-2011, 09:40 PM
Replies: 9
Views: 5,003
Posted By rururara
i try artemis and tablet but i failed to view in...

i try artemis and tablet but i failed to view in IGV even though I already sorted and index the BAM file.
any tips can you share with me to view in IGV because so many times i tried but still can't...
Forum: Bioinformatics 02-24-2011, 11:52 PM
Replies: 1
Views: 2,248
Posted By rururara
mate unmapped and read unmapped

Hi,

Can anyone here explain what is mate unmapped and read unmapped?
Thanks!
Forum: Bioinformatics 02-23-2011, 05:20 PM
Replies: 3
Views: 2,561
Posted By rururara
Failed to View .BAM file in Artemis

I always get this error when I view .BAM file in Artemis. I create the index file in the same folder. The error message I got : .bam.bai is older than .bam file .
I dont have any idea about this....
Showing results 1 to 25 of 31

 


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