User: dr.ks.iitkgp

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Posts by dr.ks.iitkgp

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Answer: A: How to calculate percentage of indels in vcf file generated after mpileup on bam
... Hi Jen, Thanks for the answer. I have one more question. Supposedly, all the steps (like PCRs, PCR-duplication removal, alignment quality filtering, sequencing errors or misalignments) have been taken into account perfectly or almost perfectly. Can we consider IMF values equivalent to frequency of ...
written 2.8 years ago by dr.ks.iitkgp0
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How to calculate percentage of indels in vcf file generated after mpileup on bam files?
... We used genome editing nucleases to alter a specific site. Use of genome editing nucleases led to indel formation in the mouse genome. Further, I performed PCR at the site of interest and performed illumina deep sequencing. My aim is to calculate frequency and indels in the bam files generated after ...
vcf mpileup indel indels written 2.8 years ago by dr.ks.iitkgp0
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Error in exporting work flow with galaxy
... I created a workflow with samtools and vcffilter in galaxy. When I tried to export the work flow to svg format. The following error appeared - XML Parsing Error: no element found Location: https://usegalaxy.org/workflow/gen_image?id=b52561ed53c305db Line Number 1, Column 1: Consequently, I was not ...
ngs written 2.8 years ago by dr.ks.iitkgp0 • updated 2.8 years ago by Dannon Baker3.7k
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To determine frequency of crispr cas induced indels in bam files
... I have used CRISPR/Cas molecules to target a specific gene. I want to quantify the frequency of indels as a result of targeting by CRISPR/Cas using galaxy or any other easier tool. I already have my bam files ready. Now, I need to align and find frequency of indels in these BAM files. Can anyone giv ...
galaxy written 2.8 years ago by dr.ks.iitkgp0 • updated 2.8 years ago by Bjoern Gruening5.1k

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