Forum: Bioinformatics
03-14-2013, 09:02 PM
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Replies: 4
Views: 1,528
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Forum: SOLiD
03-26-2012, 08:41 PM
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Replies: 34
Views: 29,641
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Forum: Bioinformatics
07-27-2011, 12:04 PM
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Replies: 11
Views: 8,186
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Forum: Bioinformatics
07-27-2011, 10:14 AM
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Replies: 11
Views: 8,186
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Forum: Bioinformatics
07-27-2011, 07:32 AM
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Replies: 11
Views: 8,186
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...
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Forum: Bioinformatics
07-06-2011, 10:54 AM
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Replies: 2
Views: 3,293
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Forum: Bioinformatics
07-05-2011, 01:19 AM
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Replies: 39
Views: 11,443
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Forum: Illumina/Solexa
07-10-2010, 07:44 AM
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Replies: 11
Views: 4,005
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...
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Forum: Illumina/Solexa
07-08-2010, 10:04 PM
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Replies: 11
Views: 4,005
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...
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Forum: Bioinformatics
07-06-2010, 08:39 AM
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Replies: 2
Views: 4,857
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...
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Forum: Illumina/Solexa
07-06-2010, 03:08 AM
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Replies: 11
Views: 4,005
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,...
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Forum: Bioinformatics
06-26-2010, 11:24 PM
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Replies: 16
Views: 6,172
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Forum: Bioinformatics
10-08-2009, 08:22 PM
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Replies: 27
Views: 39,621
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....
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Forum: Bioinformatics
10-08-2009, 07:58 PM
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Replies: 27
Views: 39,621
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Forum: Bioinformatics
10-08-2009, 04:32 AM
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Replies: 27
Views: 39,621
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Forum: Illumina/Solexa
10-07-2009, 03:54 AM
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Replies: 1
Views: 3,758
"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...
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Forum: Bioinformatics
10-07-2009, 03:31 AM
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Replies: 27
Views: 39,621
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Forum: Bioinformatics
10-07-2009, 02:37 AM
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Replies: 27
Views: 39,621
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(/^[\>\@]/){
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Forum: Bioinformatics
10-07-2009, 02:01 AM
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Replies: 27
Views: 39,621
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...
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Forum: SOLiD
10-05-2009, 10:35 PM
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Replies: 34
Views: 29,641
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"...
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Forum: Bioinformatics
09-16-2009, 05:34 AM
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Replies: 2
Views: 2,449
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Forum: Illumina/Solexa
09-15-2009, 04:29 AM
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Replies: 14
Views: 3,721
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Forum: Bioinformatics
09-14-2009, 01:59 AM
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Replies: 26
Views: 8,868
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...
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Forum: Bioinformatics
09-11-2009, 08:44 PM
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Replies: 26
Views: 8,868
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Forum: Bioinformatics
09-07-2009, 08:19 AM
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Replies: 26
Views: 8,868
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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