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Forum: Bioinformatics 10-20-2017, 12:53 AM
Replies: 0
Views: 630
Posted By edge
Scaffolding assembly contig with various Mate pair Library Inquiry

I have a sets of Illumina pair-end data sets and used it as input file for de-novo genome assembler program.
I have generate corresponding assembly contigs and I plan to run SSPACE for scaffolding...
Forum: RNA Sequencing 03-20-2014, 06:23 PM
Replies: 2
Views: 1,267
Posted By edge
Hi TiborNagy, Thanks for advice. I will...

Hi TiborNagy,

Thanks for advice.
I will have a try on it now.

Hope it works.
Forum: RNA Sequencing 03-19-2014, 08:45 PM
Replies: 2
Views: 1,267
Posted By edge
Problem faced to deal with multisample by using Cuffdiff

Hi,

I have 10 RNA-seq samples now.
Samples Times (hours after inoculation)
Susceptible NIL 0
Susceptible NIL 3
Susceptible NIL 6
Susceptible NIL 9
Susceptible NIL 12
Resistant NIL 0
Forum: Bioinformatics 03-19-2014, 06:47 AM
Replies: 0
Views: 1,272
Posted By edge
Inquiry about using Cuffdiff for multisample analysis

Hi,

I have 10 RNA-seq samples now.
Samples Times (hours after inoculation)
Susceptible NIL 0
Susceptible NIL 3
Susceptible NIL ...
Forum: Bioinformatics 02-04-2013, 08:32 PM
Replies: 25
Views: 9,954
Posted By edge
Hi dpryan, Do you know what is the meaning...

Hi dpryan,

Do you know what is the meaning of 20?
I run bwa to map my single-end read back to contig.
It shown 0, 4, 16, 20 in the sorted.bam T_T

Thanks for advice.
Forum: Bioinformatics 02-04-2013, 08:31 PM
Replies: 25
Views: 9,954
Posted By edge
Hi win804, Do you know what is the meaning...

Hi win804,

Do you know what is the meaning of 20?
I run bwa to map my single-end read back to contig.
It shown 0, 4, 16, 20 in the sorted.bam T_T

Thanks for advice.
Forum: Bioinformatics 01-28-2013, 01:55 AM
Replies: 25
Views: 9,954
Posted By edge
Hi dpryan, Many thanks for your reply. I...

Hi dpryan,

Many thanks for your reply.
I understand it right now :)
Forum: Bioinformatics 01-28-2013, 01:51 AM
Replies: 25
Views: 9,954
Posted By edge
Hi win804, Many thanks for your advice. I...

Hi win804,

Many thanks for your advice.
I understand it now.
Thanks again.
Forum: Bioinformatics 01-28-2013, 12:49 AM
Replies: 25
Views: 9,954
Posted By edge
Hi Yuan, Do you mind to explain what is the...

Hi Yuan,

Do you mind to explain what is the exact meaning of 0, 4, 16 if I map my single-end read against reference transcript by using bowtie?
As I know, 4 is refer to unmapped.
How about 0 and...
Forum: Bioinformatics 12-18-2012, 06:39 PM
Replies: 8
Views: 1,449
Posted By edge
I have no idea about it too :( I just...

I have no idea about it too :(

I just reported it as a bug of samtools mpileup.
I test the samtools mpileup for genome and transcriptome data set, both still same :(

Just wondering GATK got...
Forum: Bioinformatics 12-18-2012, 05:50 PM
Replies: 8
Views: 1,449
Posted By edge
Hi, Do you get any feedback or advice from...

Hi,

Do you get any feedback or advice from Samtools to solve this issue?
It really surprised me when I re-run exactly the same data set and same command for few times.
Every time it gives...
Forum: Bioinformatics 12-18-2012, 04:52 PM
Replies: 8
Views: 1,449
Posted By edge
Samtools mpileup generate different SNP result every run?

Hi,

I just wondering is it normal that re-run exactly the same data set by using exactly same command will generate different SNP calling result?

Currently I notice that if I re-run SNP calling...
Forum: Bioinformatics 12-05-2012, 07:45 PM
Replies: 2
Views: 1,639
Posted By edge
Thanks BAMseek. You are right. You solved...

Thanks BAMseek.

You are right.
You solved my problem instead :)

Many thanks.
Forum: Bioinformatics 12-05-2012, 07:24 AM
Replies: 2
Views: 1,639
Posted By edge
Cmake (ensure_out_of_source_build) error

Currently I would like to install bamtools.
However, I keep on facing the following bug message:
CMake Error at CMakeLists.txt:20 (message):


BamTools requires an out of source build.
...
Forum: Bioinformatics 11-25-2012, 11:50 PM
Replies: 12
Views: 9,762
Posted By edge
Hi giorgifm, Thanks for your advice. ...

Hi giorgifm,

Thanks for your advice.

Below is the criteria of my data set and problem facing right now:
I have 2 sets of Illumina pair-end RNA-seq data which shown as below:
1. normal tissue...
Forum: Bioinformatics 11-25-2012, 11:25 PM
Replies: 12
Views: 9,762
Posted By edge
Hi giorgifm, Do you mind to share more...

Hi giorgifm,

Do you mind to share more regarding how you calling SNP by using VarScan?
If can, hope you can explain on it more detail.
Thanks.
Forum: Bioinformatics 11-25-2012, 08:31 PM
Replies: 34
Views: 123,878
Posted By edge
Hi, As I know due to inherent mistakes in...

Hi,

As I know due to inherent mistakes in the sequencing technology, some reads will be exact copies of each other. They share the same sequence and the same alignment position and could cause...
Forum: Bioinformatics 11-25-2012, 04:53 PM
Replies: 11
Views: 10,691
Posted By edge
Thanks, dpryan. I will have a look on the...

Thanks, dpryan.

I will have a look on the document that you shared.
Really appreciate :)
Forum: Bioinformatics 11-25-2012, 12:20 AM
Replies: 11
Views: 10,691
Posted By edge
Hi. Thanks for answer about 255 by bowtie...

Hi.

Thanks for answer about 255 by bowtie sam output.

Hi,

Do you know what is the meaning of 100M from bowtie sam output?
I run bowtie with single-read.
My input file is 100 read length.
Forum: Bioinformatics 11-25-2012, 12:20 AM
Replies: 11
Views: 10,691
Posted By edge
Hi, Do you know what is the meaning of 100M...

Hi,

Do you know what is the meaning of 100M from bowtie sam output?
I run bowtie with single-read.
My input file is 100 read length.

Thanks.
Forum: Bioinformatics 11-25-2012, 12:01 AM
Replies: 48
Views: 51,573
Posted By edge
Hi, Is it 16 refer to read map at reverse...

Hi,

Is it 16 refer to read map at reverse strand?
Can I know which bitwise flag refer to those read that map in pair?

Thanks.
Forum: Bioinformatics 11-24-2012, 04:30 AM
Replies: 0
Views: 767
Posted By edge
How to assess Phrap assembly result

Hi,

Currently I was running Phrap for re-assemble of my transcriptome data-set.
The command that I run for Phrap is shown as below:
phrap -minscore 100 -ace assembly.contig.fna

Can I know how...
Forum: Bioinformatics 11-24-2012, 03:11 AM
Replies: 12
Views: 6,989
Posted By edge
Hi, Can you email me a copy of the paper...

Hi,

Can you email me a copy of the paper that you mention regarding "how to assess a de novo assembly result?"?
Many thanks.

I can't access it too :(
Forum: Bioinformatics 09-20-2012, 06:38 AM
Replies: 4
Views: 5,838
Posted By edge
I used the latest version of Varscan. The...

I used the latest version of Varscan.
The mpileup is replaced the pileup right now.
I able to run Varscan right now.
The above error is due to the problem of my java version :(

Apart from that,...
Forum: Bioinformatics 09-20-2012, 06:33 AM
Replies: 1
Views: 1,609
Posted By edge
I got two sets of Illumina pair-end transcriptome...

I got two sets of Illumina pair-end transcriptome data (both set are closely-related plant species). First, I will trim adaptor sequence and low quality bases of both data set separately before...
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