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I am working on a CRISPR data treated by two sgRNAs and sequenced with targeted sequencing. The distance between the two sgRNA is 3000bp which is much longer than amplicon. The targeted area is the w…
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Hi there,
I would like to apply OFF-PEAK to some targeted EM-seq data (obtained using the Twist Methylome Panel). However, since the tool was designed specifically for exome sequencing data, all ta…
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Hi,
I'm trying to simulate reads for individual genes. However I noticed that after aligning, the read depth in the first few hundred and the last few hundred bases of each reference sequence is lowe…
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Hi, I am using smoove to call SVs. I have about 50 samples, which are tumor-normal pairs of human. Their sequencing depth is about 1000X, which is targeted sequencing. I want to know if I can use smoo…
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This has been sitting around as a possibility for some time; we should just do it.
I propose
1. Chuck out species id
2. Update genome size to be lengths of genes in our targets (allow user speci…
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Dear All,
Can I use Mykrobe tool for targeted sequencing instead of whole genome sequencing?
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I am applying CNVkit to targeted amplicon sequencing data by following your command:
cnvkit.py batch -m amplicon -t targets.bed *.bam
Is this command using the default bin size of 200?
Some of …
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Hi, I found that for targeted amplicon sequencing data, the mutations called by Pisces 5.2.7.47 will mostly be flagged as 'SB'. Is it a property of amplicon sequencing data or primer specificity? how …
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I saw in #7 that for amplicon-awared variant calling, the BED file need to have 8 columns storing both the primer and insert positions. However, the BED file that comes with the manufacturer's target…
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Hi,
I have successfully used DISCOVER with data from whole-exome sequencing. I am wondering whether I can use it with data from targeted sequencing data generated by MSK IMPACT or DFCI OncoPanel. A…
jud-b updated
6 months ago