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Forum: Bioinformatics 03-19-2012, 06:15 PM
Replies: 34
Views: 136,595
Posted By dongshenglulv
Why did the "recurrent sequencing errors seems to...

Why did the "recurrent sequencing errors seems to be caused by PCR?
Forum: Bioinformatics 03-19-2012, 06:13 PM
Replies: 34
Views: 136,595
Posted By dongshenglulv
Why did the "recurrent sequencing errors" is...

Why did the "recurrent sequencing errors" is likely to be caused by PCR?
Forum: Bioinformatics 11-20-2011, 05:06 AM
Replies: 3
Views: 12,390
Posted By dongshenglulv
Thanks very much, I've already done by what...

Thanks very much, I've already done by what you've suggested.
Forum: Bioinformatics 11-18-2011, 09:42 PM
Replies: 3
Views: 12,390
Posted By dongshenglulv
error in picard (SAM validation error)

Hi, I had a error message when I use picard to replace read groups in a BAM file, like this:

$ java -jar AddOrReplaceReadGroups.jar I=SRX020270.sorted.bam O=SRX020270.resorted.bam ...
Forum: Bioinformatics 05-22-2011, 06:40 AM
Replies: 8
Views: 3,848
Posted By dongshenglulv
The only parameter for criteria here is -D. I...

The only parameter for criteria here is -D. I just tried this command,
$ samtools mpileup -P ILLUMINA -ugf hg19.fasta *.bam | bcftools view -cvg - > var.raw.vcf

Then the standard output was the...
Forum: Bioinformatics 05-20-2011, 06:14 AM
Replies: 5
Views: 12,047
Posted By dongshenglulv
Thanks very much, it's solved

Thanks very much, it's solved
Forum: Bioinformatics 05-19-2011, 06:23 PM
Replies: 8
Views: 3,848
Posted By dongshenglulv
*.bam -> var.bcf No result

Hi all,

When I tried to call variants by 25 BAM files like this,
$ samtools mpileup -P ILLUMINA -ugf hg19.fasta *.bam | bcftools view -bcvg - > var.raw.bcf ; bcftools view var.raw.bcf |...
Forum: Bioinformatics 05-18-2011, 10:06 PM
Replies: 5
Views: 12,047
Posted By dongshenglulv
Actually I did. I'm using the samtools (0.1.16), ...

Actually I did. I'm using the samtools (0.1.16),
Here is my command line,

$ samtools view -bt hg19.fa.fai unsorted.sam -o unsorted.bam
note that the unsorted.sam has no header @SQ

then I...
Forum: Bioinformatics 05-18-2011, 08:45 PM
Replies: 5
Views: 12,047
Posted By dongshenglulv
the header of SAM and BAM missing

Hi

I use the soap2sam.pl to convert the soap file file.soap to file.sam, but the header in file.sam is missing, so I have to add the header to the file.sam. When I convert this file.sam to...
Forum: Illumina/Solexa 05-14-2011, 03:04 AM
Replies: 74
Views: 399,760
Posted By dongshenglulv
Did you mean that the difference between PE and...

Did you mean that the difference between PE and SE is that PE sequencing can do the 'desired cycle-count' twice? Meanwhile, did you mean that the cell flow is not disposable, we can reuse it for...
Forum: Personalized Genomics 05-12-2011, 08:19 PM
Replies: 2
Views: 8,662
Posted By dongshenglulv
The site for Watson's genome download

Hi all,

I want to download the genome sequence of personal sequencing to date. I just know that Watson, and a Asian guy's genome have been sequenced. Does anybody know the ftp site for these...
Forum: Bioinformatics 05-12-2011, 07:02 PM
Replies: 3
Views: 6,497
Posted By dongshenglulv
quality control from fastq to vcf

Hi all,

This is my framework to call SNP from 50 fastq files,
1> use bowtie to get SAM from fastq. reference genome: hg19.fa, paras in bowtie: -k 2 -v 2. Then I have 50 SAM files
2> convert SAM...
Forum: Illumina/Solexa 05-12-2011, 05:40 AM
Replies: 4
Views: 5,014
Posted By dongshenglulv
Thank you so much

Thank you so much
Forum: Illumina/Solexa 05-11-2011, 11:58 PM
Replies: 4
Views: 5,014
Posted By dongshenglulv
Solexa and HiSeq

I'm very confused with the relationship of Solexa and HiSeq.
Is it true that HiSeq 2000 based on the technology of Solexa?
Forum: Illumina/Solexa 05-11-2011, 09:51 PM
Replies: 74
Views: 399,760
Posted By dongshenglulv
That's what I'm looking for. Thank you so much

That's what I'm looking for. Thank you so much
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