User: C Shao

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C Shao130
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Posts by C Shao

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Tophat Mapping Rate With Rna-Seq.
... Thanks, I will try with default value, then see how it happens. ...
written 8.0 years ago by C Shao130
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Comment: C: Tophat Mapping Rate With Rna-Seq.
... According to your explanation, I set "-g 1" to let tophat report only one mapped reads even if reads are mapped in multiple position. Then, for example, I set "-g 2" , and selecte reas with "NH i 1", which will give the uniquely mapped reads. Is it a paradox? I also see many people in seqanswers s ...
written 8.0 years ago by C Shao130
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Comment: C: Tophat Mapping Rate With Rna-Seq.
... I want to get the read counts for each genes, then analyze them with linear model under poisson distribution. That is why I want the uniquely mapped reads. How do you work with tophat? Do you know any way to get the uniquely mapped reads? ...
written 8.0 years ago by C Shao130
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Tophat Mapping Rate With Rna-Seq.
... I am confused about my RNA-seq mapping results from tophat. It's pair-end sequencing data, 101 bp length from Hiseq 2000. Here is the command I used: tophat -p 8 -g 1 -G $geneInfo -o $examp_thout $bowtie2in $fastqP1 $fastqP2 "-g 1" specified that only uniquely mapped reads are kept; "$geneInfo" ...
tophat rna-seq written 8.0 years ago by C Shao130 • updated 8.0 years ago by Istvan Albert ♦♦ 86k
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How To Use R To Segment Genome And Count Reads From Sequencing Data?
... Hi everyone: I have some whole-genome sequencing data, now I would like to segment human genome (1:22, X,Y) to nonoverlap equal size bins and count reads within it, defining by the location of fire base of one read. What to do this only through R? I am trying Rsamtools but didn't get any solutio ...
written 8.3 years ago by C Shao130 • updated 8.3 years ago by Michael Dondrup48k
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Comment: C: How To Check Structure Variation In Igv Or Other Tools?
... Yes, and I think I have deleted my post. Wired. ...
written 8.3 years ago by C Shao130
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How To Check Structure Variation In Igv Or Other Tools?
... I found many structure variations in the genome sequencing data by breakdancer. Now I am trying to evaluate them visually. However, the breakdancer seems not to provide information on which pair of reads support the translocation, or other SV. For the information provided by IGV, they are many rea ...
deleted-post written 8.3 years ago by C Shao130 • updated 5.5 years ago by Biostar ♦♦ 20
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Target Region For Agilent Early Access Human All Exon V4
... Does anyone know where to find the target region of "Agilent Early Access Human All Exon V4"? From the website I only get the description for the kit, but cant find any link to the target region. We used this kit for our exome sequencing, now we hope to use it for calculating coverage. Thanks. ...
agilent written 8.4 years ago by C Shao130
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Experience Needed For Snp Calling By Samtools/Bcftools
... Hi everyone: I have successfully found some snps from whole exome data, mainly through samtools. But I want to make a shorter list containing the more convincing snps. I guess read depth is important, what else should I consider? I would like to hear your experience and suggestions. How did yo ...
samtools bcftools snp written 8.5 years ago by C Shao130 • updated 8.5 years ago by Zev.Kronenberg11k
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Comment: C: How To Interpret -D File In Samtools Variant Calling Pipeline?
... My understanding is that if unique or "reliable" (from FAQ of samtools ) sequences are used for snp calling, the -D option is meaningless, since the high coverage is not caused by duplication of genome segments. ...
written 8.5 years ago by C Shao130

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