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Search: Posts Made By: BENM
Forum: Bioinformatics 03-14-2013, 08:02 PM
Replies: 4
Views: 1,402
Posted By BENM
It is most likely plotted by PERL GD module. R,...

It is most likely plotted by PERL GD module. R, gnuplot, python mathplotlib also can do it.
Forum: SOLiD 03-26-2012, 07:41 PM
Replies: 34
Views: 28,714
Posted By BENM
I have already fixed some bugs of it, you can try...

I have already fixed some bugs of it, you can try it again.
Forum: Bioinformatics 07-27-2011, 11:04 AM
Replies: 11
Views: 7,589
Posted By BENM
Yes, you're right. Sorry, I didn't pay attention...

Yes, you're right. Sorry, I didn't pay attention to your code.
Forum: Bioinformatics 07-27-2011, 09:14 AM
Replies: 11
Views: 7,589
Posted By BENM
Hi boetsie, you would find out you missed the...

Hi boetsie, you would find out you missed the last sequence.
Forum: Bioinformatics 07-27-2011, 06:32 AM
Replies: 11
Views: 7,589
Posted By BENM
Try this run in your terminal: perl -e 'my...

Try this run in your terminal:

perl -e 'my ($name,$seq)=("","");while(<>){chomp;if ((/\>/)||(eof)){if (($seq ne "")||(eof)){$seq.=$_ if (eof);my @Seq=split /N+/,$seq;if (@Seq>1){for my...
Forum: Bioinformatics 07-06-2011, 09:54 AM
Replies: 2
Views: 3,159
Posted By BENM
it looks like it can't find zlib on your system,...

it looks like it can't find zlib on your system, and did you install c/c++ compiler and SDK at your Mac, like xcode?
Forum: Bioinformatics 07-05-2011, 12:19 AM
Replies: 39
Views: 11,015
Posted By BENM
hi, do you mean experiment normalization or data...

hi, do you mean experiment normalization or data normalization for quantification analysis?

If it is for cDNA libraries normalization, one of application is duplex-specific nuclease (DSN), which...
Forum: Illumina/Solexa 07-10-2010, 06:44 AM
Replies: 11
Views: 3,768
Posted By BENM
Hello pratibhamani, If you have enough...

Hello pratibhamani,

If you have enough sequencing coverage, it is no need to worry about the error rate of sequencing quality. Because in de Bruijn graphs algorithm, it can deal with them by...
Forum: Illumina/Solexa 07-08-2010, 09:04 PM
Replies: 11
Views: 3,768
Posted By BENM
It is due to Assembly tools you use. But for...

It is due to Assembly tools you use.
But for Solexa reads, there is just lower than 1% error rates. So these reads with high error rates must be in lower coverage, then they still can be figured out...
Forum: Bioinformatics 07-06-2010, 07:39 AM
Replies: 2
Views: 4,618
Posted By BENM
I think you'd better to run sampe for each PE...

I think you'd better to run sampe for each PE files separately:

bwa sampe [options] <prefix> <in1.sai> <in2.sai> <in1.fq> <in2.fq>

Although you concatenate all read files into two PE seq is...
Forum: Illumina/Solexa 07-06-2010, 02:08 AM
Replies: 11
Views: 3,768
Posted By BENM
Hi ritzriya, I can give you an simple script...

Hi ritzriya,

I can give you an simple script for quality control, which can filter out the low quality sequence or N's reads, it due to the option you set:
-n N's content of the reads,...
Forum: Bioinformatics 06-26-2010, 10:24 PM
Replies: 16
Views: 5,911
Posted By BENM
Hello DrD2009, Are your sequences TagSeq or...

Hello DrD2009,

Are your sequences TagSeq or other else?
If you just want to get the uniue sequence in whole length of reads, you can just use the command in Linux:
awk '{if...
Forum: Bioinformatics 10-08-2009, 07:22 PM
Replies: 27
Views: 37,637
Posted By BENM
Hi Edge, I don't think I am PERL programmer...

Hi Edge,

I don't think I am PERL programmer expert, just a junior learner.
It is the same as python or C/C++, or other program language, I think the most important is algorithm or thinking idea....
Forum: Bioinformatics 10-08-2009, 06:58 PM
Replies: 27
Views: 37,637
Posted By BENM
hi Edge, The "calengc.pl" has a bug in stat....

hi Edge,

The "calengc.pl" has a bug in stat. gc content, it has been corrected.
Forum: Bioinformatics 10-08-2009, 03:32 AM
Replies: 27
Views: 37,637
Posted By BENM
hi edge, I have written a PERL script for...

hi edge,

I have written a PERL script for stat. length and gc content of FASTA/FASTQ file, hope it ould help you.
Forum: Illumina/Solexa 10-07-2009, 02:54 AM
Replies: 1
Views: 3,624
Posted By BENM
"Although indexing has the obvious benefit of...

"Although indexing has the obvious benefit of multiplexing samples within a run, DNA indexing offers two key additional advantages: direct measure of base-by-base error rate and reduction of...
Forum: Bioinformatics 10-07-2009, 02:31 AM
Replies: 27
Views: 37,637
Posted By BENM
I am using this software, but not familiar. There...

I am using this software, but not familiar. There are *_out.padded.fasta and *_out.unpadded.fasta in the ouput directory of "projectname_d_result". It defined contigs lenth >=500bp are large contigs....
Forum: Bioinformatics 10-07-2009, 01:37 AM
Replies: 27
Views: 37,637
Posted By BENM
hi edge, I am sorry for a little mistake,...

hi edge,

I am sorry for a little mistake, you can type the below code into a perl script:

#/usr/bin/perl -w
use strict;
my ($len,$total)=(0,0);
my @x;
while(<>){
if(/^[\>\@]/){
Forum: Bioinformatics 10-07-2009, 01:01 AM
Replies: 27
Views: 37,637
Posted By BENM
N50 = length-weighted median.: The size of the...

N50 = length-weighted median.: The size of the smallest contig such that 50% of the length of the genome is contained in contigs of size N50 or greater.
N90 is 90%.
If you have done the assembly...
Forum: SOLiD 10-05-2009, 09:35 PM
Replies: 34
Views: 28,714
Posted By BENM
Hi inesdesantiago Thank you for your...

Hi inesdesantiago

Thank you for your opinions. In color space if one color space can't be recognized by SOLiD™ System, it will cause the rear bases uncertain too. So, the reads will decode "N"...
Forum: Bioinformatics 09-16-2009, 04:34 AM
Replies: 2
Views: 2,241
Posted By BENM
Hi, Marian I have a PERL script here, hope it...

Hi, Marian
I have a PERL script here, hope it will help you.
Command: perl phraplist.pl phrap.out > phrap.list

#!/usr/bin/perl
#phraplist.pl
die "Usage:$0 phrap.out\n" if (@ARGV!=1);...
Forum: Illumina/Solexa 09-15-2009, 03:29 AM
Replies: 14
Views: 3,372
Posted By BENM
May be you can find the answer at this papers "H....

May be you can find the answer at this papers "H. Alexander Ebhardt etc. al., Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications, Nucleic Acids...
Forum: Bioinformatics 09-14-2009, 12:59 AM
Replies: 26
Views: 8,263
Posted By BENM
Hi Patrick, You're welcome. In fact I am...

Hi Patrick,

You're welcome.
In fact I am one of the co-authors of this paper, thereinto the SV detetion of this project is my main job. But I am not in BGI now.
About the main finding from the...
Forum: Bioinformatics 09-11-2009, 07:44 PM
Replies: 26
Views: 8,263
Posted By BENM
I am sorry for a prompt reply, there is a list of...

I am sorry for a prompt reply, there is a list of tenology approach & reference for detecting SV here, hope it help to you.

(1)GTG-banded karyotype
The gold standard for clinical cytogenetic...
Forum: Bioinformatics 09-07-2009, 07:19 AM
Replies: 26
Views: 8,263
Posted By BENM
In 1000 Genomes Project there are 50% false...

In 1000 Genomes Project there are 50% false positives in SV detection, so it is worth to pay more attentions to this field. Rather than use CNV BeadChip or PEM(alignment algorithm), maybe assembly is...
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