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Forum: Bioinformatics 08-26-2013, 03:08 AM
Replies: 7
Views: 1,417
Posted By dkrtndhkd
yes, i read the article you linked. as i...

yes, i read the article you linked.

as i understood,



from this, they validated the newly found ORIs.
Forum: Bioinformatics 08-24-2013, 07:30 PM
Replies: 7
Views: 1,417
Posted By dkrtndhkd
oh, i'm confused the term, replication fork and...

oh, i'm confused the term, replication fork and origin of replication.

i'm sorry... thank you i learned a new concept.

then, question again; the position of the origin of replication is fixed?...
Forum: Bioinformatics 08-24-2013, 08:41 AM
Replies: 1
Views: 5,132
Posted By dkrtndhkd
EST, microarray, RNAseq difference?

I want to know the difference of EST, microarray, RNAseq.

this is my conclusion;

through EST, we can know the sequence of transcripts from each cell type,
and from the result of EST, we can...
Forum: Bioinformatics 08-24-2013, 08:35 AM
Replies: 7
Views: 1,417
Posted By dkrtndhkd
Oh, it's interesting... until now, I knew...

Oh, it's interesting...

until now, I knew that replication fork site(ORC1 binding site) is fixed.

thank you for your reply!
Forum: Bioinformatics 08-23-2013, 04:54 PM
Replies: 7
Views: 1,417
Posted By dkrtndhkd
no, in homo sapiens!

no, in homo sapiens!
Forum: Bioinformatics 08-23-2013, 07:59 AM
Replies: 7
Views: 1,417
Posted By dkrtndhkd
How can i get replication fork's position?

I want to know the position of replication fork of each chromosome.

ex)chr 1:bp10000, bp120000...
chr 2:bp 11000, bp 100000...

I searched about it from NCBI, UCSC but I could not get it....
Forum: Bioinformatics 08-21-2012, 09:56 PM
Replies: 10
Views: 2,350
Posted By dkrtndhkd
and, if the paired-end read sequencing result...

and, if the paired-end read sequencing result anyway comes from 1 fragment with various length(for example, 150~500bp),

the aligned position of two read(1 forward read, 1 reverse read and they...
Forum: Bioinformatics 08-21-2012, 09:52 PM
Replies: 10
Views: 2,350
Posted By dkrtndhkd
Oh, thank you. I had an wrong understanding about...

Oh, thank you. I had an wrong understanding about paired-end sequencing.

then, each fragment does not have uniform length, why paired-end sequencing was developed?

the length that sequencing...
Forum: Bioinformatics 08-21-2012, 07:40 AM
Replies: 10
Views: 2,350
Posted By dkrtndhkd
Thank you westerman!!! Your second reply was...

Thank you westerman!!!

Your second reply was what i wanted to ask.

and, further question!

I understand that for reason of less error prone, illumina makes two(paired-end) fastq files.

but...
Forum: Bioinformatics 08-20-2012, 09:18 AM
Replies: 10
Views: 2,350
Posted By dkrtndhkd
Yes, I use bwa aligner and how to use it. ...

Yes, I use bwa aligner and how to use it.

this post is about the 'concept' of paired-end read process.

I don't understand why they don't merge for/rev fastq and align them seperately.
Forum: Bioinformatics 08-19-2012, 11:19 PM
Replies: 10
Views: 2,350
Posted By dkrtndhkd
paired-end mapping and SAM info.

Hi, I have an fundamental question...

as you know, paired-end fastq files(ex. 'asdf.for.fastq' and 'asdf.rev.fastq') can be aligned to 'asdf.sam'

As I know, aligner program aligns each forward...
Forum: Bioinformatics 08-14-2012, 06:36 PM
Replies: 7
Views: 2,194
Posted By dkrtndhkd
because in my pipeline, i use ANNOVAR tool for...

because in my pipeline, i use ANNOVAR tool for annotation step and ANNOVAR gets input file with VCF format:(

I know I can change some column to make input file(vcf4.0 format) for ANNOVAR,

but I...
Forum: Bioinformatics 08-14-2012, 10:13 AM
Replies: 7
Views: 2,194
Posted By dkrtndhkd
thank you

Thank you!!!!

I see it now because the alarm mail was in spam box...:(

another question!

is there any option of MuTect to get output with VCF format???
Forum: Bioinformatics 08-09-2012, 09:00 AM
Replies: 1
Views: 2,463
Posted By dkrtndhkd
how can i interpret the result of mpileup of samtools?

for example,
7 151843760 T 33 .$,$,....,.,......,.,..,..,,..,,,.^g, >@FDCDDJEIDDEIHGJAJJIEJJFEIHDDDCC

I know the col1=chromosome, col2=base position col3=reference seq col4=depth

but what's...
Forum: Bioinformatics 08-05-2012, 03:14 AM
Replies: 2
Views: 1,219
Posted By dkrtndhkd
Yes! i mean it

Yes! i mean it
Forum: Bioinformatics 08-04-2012, 12:04 PM
Replies: 2
Views: 1,219
Posted By dkrtndhkd
Does BWA cannot align reads to fasta with RYWSM?

Hi, I have a simple question!

Does BWA cannot align reads to fasta sequence with RYWSM?

Thank you!
Forum: Bioinformatics 08-03-2012, 08:58 PM
Replies: 7
Views: 2,194
Posted By dkrtndhkd
annovar output - the meaning of REJECT?

Hi,

I want to know the meaning of 'REJECT' of output file of ANNOVAR like follow:

line2 nonsynonymous...
Forum: Bioinformatics 08-03-2012, 08:56 AM
Replies: 2
Views: 2,213
Posted By dkrtndhkd
MuTect -> vcf pipeline?option?

Hi, is there anyone who know the option of MuTect which gives a VCF formed result to users?

I know that we can modify the result of MuTect by switching and copying certain column,

but the extra...
Forum: Bioinformatics 08-03-2012, 08:27 AM
Replies: 2
Views: 1,131
Posted By dkrtndhkd
thank you :)

thank you :)
Forum: Bioinformatics 07-31-2012, 07:22 PM
Replies: 2
Views: 1,131
Posted By dkrtndhkd
is anyone who have used MuSiC in WashU?

Hello, I'm first in using MuSiC tool and got a problem.

when I calculate bmr, I used calc-bmr option and put parameters as the synopsis of website says.

however, I got this error messege;
...
Forum: Bioinformatics 05-04-2012, 08:39 PM
Replies: 5
Views: 4,930
Posted By dkrtndhkd
what about somatic option?? I couldn't find...

what about somatic option??

I couldn't find the vcf file output option command...
Forum: Bioinformatics 04-29-2012, 09:03 AM
Replies: 3
Views: 2,122
Posted By dkrtndhkd
Thank you:) and futher question... the...

Thank you:)

and futher question...

the word 'ignored' means that Annovar didn't annotate any gene name and just deleted the SNP??
Forum: Bioinformatics 04-26-2012, 11:48 PM
Replies: 5
Views: 4,930
Posted By dkrtndhkd
Smile varscan-annotation pipeline?

How to connect VarScan output and annotation tools?

is there any useful tool to directly annotate the varscan's output file?

or I have to change the form of the output file to vcf format?
Forum: Bioinformatics 04-26-2012, 10:48 PM
Replies: 3
Views: 2,122
Posted By dkrtndhkd
Post annovar output - question

I run annovar to annotate my snp file.

I saw this message:

WARNING: A total of 273 sequences will be ignored due to lack of correct ORF annotation

somebody please let me know what's the...
Forum: Bioinformatics 03-24-2012, 03:31 AM
Replies: 1
Views: 1,484
Posted By dkrtndhkd
making reference from ucsc : include or not - chrUn

Hi, I have simple question.

i'm using hg19 reference from ucsc.

i downloaded 93 chr*.fa file (1~23, X, Y, MT, Un_*, gl*);
chr1.fa
chr10.fa
chr11.fa
chr11_gl000202_random.fa
chr12.fa
Showing results 1 to 25 of 42

 


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