Forum: Bioinformatics
03-19-2012, 06:15 PM
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Replies: 34
Views: 136,595
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Forum: Bioinformatics
03-19-2012, 06:13 PM
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Replies: 34
Views: 136,595
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Forum: Bioinformatics
11-20-2011, 05:06 AM
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Replies: 3
Views: 12,390
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Forum: Bioinformatics
11-18-2011, 09:42 PM
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Replies: 3
Views: 12,390
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 ...
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Forum: Bioinformatics
05-22-2011, 06:40 AM
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Replies: 8
Views: 3,848
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...
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Forum: Bioinformatics
05-20-2011, 06:14 AM
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Replies: 5
Views: 12,047
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Forum: Bioinformatics
05-19-2011, 06:23 PM
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Replies: 8
Views: 3,848
*.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 |...
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Forum: Bioinformatics
05-18-2011, 10:06 PM
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Replies: 5
Views: 12,047
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Forum: Bioinformatics
05-18-2011, 08:45 PM
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Replies: 5
Views: 12,047
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...
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Forum: Illumina/Solexa
05-14-2011, 03:04 AM
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Replies: 74
Views: 399,760
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Forum: Personalized Genomics
05-12-2011, 08:19 PM
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Replies: 2
Views: 8,662
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...
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Forum: Bioinformatics
05-12-2011, 07:02 PM
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Replies: 3
Views: 6,497
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...
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Forum: Illumina/Solexa
05-12-2011, 05:40 AM
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Replies: 4
Views: 5,014
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Forum: Illumina/Solexa
05-11-2011, 11:58 PM
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Replies: 4
Views: 5,014
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?
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Forum: Illumina/Solexa
05-11-2011, 09:51 PM
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Replies: 74
Views: 399,760
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