Forum: Bioinformatics
03-17-2014, 02:32 AM
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Replies: 11
Views: 5,437
Hi All,
I have a bam file that containg only...
Hi All,
I have a bam file that containg only information for chr21.
When I run sh bam2coverage.sh
command :
sh bam2coverage.sh /path for bam file/chr21.sortedpicard.rmdup.realigned.recal.bam...
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Forum: RNA Sequencing
05-23-2013, 12:22 AM
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Replies: 2
Views: 3,145
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Forum: De novo discovery
04-25-2012, 07:27 PM
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Replies: 10
Views: 3,658
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Forum: De novo discovery
04-25-2012, 07:24 PM
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Replies: 10
Views: 3,658
When I try running with -I option at BWA...
When I try running with -I option at BWA alignment and converted to sam file then to bam file error occurs.
These are the comment
SEQUENCE ALIGNMENT
$ ./bwa aln -I -t 4...
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Forum: De novo discovery
03-30-2012, 11:39 PM
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Replies: 10
Views: 3,658
parameter set of bwa-samtools for snp calling
Hi,
Everyone, I use bwa-samtools for human genome SNPs calling, but the SRA READS are performed using the Illumina Genome Analyzer Pipeline v.1.4.0 software suite. Should I need to run BWA alignment...
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Forum: Bioinformatics
09-30-2011, 02:43 AM
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Replies: 29
Views: 17,407
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Forum: Bioinformatics
09-28-2011, 10:16 PM
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Replies: 29
Views: 17,407
Hello,
Before indexing hg18.fa , I put all...
Hello,
Before indexing hg18.fa , I put all chr1 to chrY including chrM to hg18.fa using this code mention below. When I tried for single chr1 fasta for indexing it runs properly. Is this error due...
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Forum: Bioinformatics
09-28-2011, 09:24 PM
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Replies: 29
Views: 17,407
Hello,
I would like to index for aligning...
Hello,
I would like to index for aligning FASTQ sequences to FASTA hg18 reference sequence. The FASTQ sample sequences are SOLID reads. Could you please assist me. I hereby attach the error...
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Forum: Bioinformatics
09-28-2011, 09:20 PM
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Replies: 29
Views: 17,407
Hello,
I would like to index for aligning...
Hello,
I would like to index for aligning FASTQ sequences to FASTA
[haojamrocky@melon bwa-0.5.9]$ ./bwa index -a bwtsw -c /home/haojamrocky/DATA/hg18chr/hg18.fasta
[bwa_index] Pack nucleotide...
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Forum: Bioinformatics
09-24-2011, 09:30 PM
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Replies: 29
Views: 17,407
Hi,
When I run BWA for aligning fasta chr.1...
Hi,
When I run BWA for aligning fasta chr.1 sequence with fastq SRR reads there is an error as below . Could you plz help me out.
Regards,
[bwa-0.5.9]$ ./bwa aln /home/DATA/chr1.fa...
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Forum: Bioinformatics
09-24-2011, 02:15 AM
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Replies: 29
Views: 17,407
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Forum: Bioinformatics
06-13-2011, 02:08 AM
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Replies: 5
Views: 2,385
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