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Posts by sheenams
... I would like to limit the base-quality-score to phred 13 (similar to default of samtools mpileup (1.3.1)), using bam-readcount (0.8.0). Despite various command modifications, I'm not getting the expected output. Default: bam-readcount -f human_g1k_v37.hotspot.fasta final.bam -l F5DNA.txt --ma ...
... Here are two that come out of a lab at University of Washington Medical Center: Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. http://www.ncbi.nlm.nih.gov/pubmed/ ...
Comment: C: Bwa Alignment Failed
... Did you do both the forward and reverse strands? bwa aln ref.fa fwd_read.fq.gz > fwd_read.sai bwa aln ref.fa rev_read.fq.gz > rev_read.sai bwa sampe ref.fa fwd_read.sai rev_read.sai fwd_read.fq.gz rev_read.fq.gz> aln.sam ...
Latest awards to sheenams
Scholar 3.6 years ago, created an answer that has been accepted. For A: Publications for individualized medicine in cancer by whole genome, exome or tra
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Publications for individualized medicine in cancer by whole genome, exome or tra
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