User: rebecca08238

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rebecca0823810
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Posts by rebecca08238

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Pipeline for SNP analysis
... yes previously I asked about filter variants in controls and patients. I used samtool pipeline (on Linux), Now I want to ask you that Can we do snp analysis in R studio? and for that which package we should download ? ...
written 7 months ago by rebecca0823810
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Comment: C: Pipeline for SNP analysis
... Thank you so much for your reply! yes NPHS1$NPHS2 are responsible for Nephrotic syndrome but there are some other genes also which are invloved in Nephrotic syndrome. which pacakage we should use for SNP analysis in R? ...
written 7 months ago by rebecca0823810
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Pipeline for SNP analysis
... Hello! I am working on Nephrotic syndrome patients. I have to check SNPs which are link with Nephrotic syndrome. study Involves 2 groups: Control, Nephrotic syndrome Work done till now: We used DNA Ampliseq illumina Library kit. Source:Genomic DNA Let me tell you in brief what I did after get ...
bcftools snp written 7 months ago by rebecca0823810 • updated 7 months ago by ATpoint32k
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Comment: C: step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... Can you please explain about soft clipping...I dont have any idea about this. ...
written 8 months ago by rebecca0823810
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Comment: C: Interpretation of SNP Analysis
... Thanks for your reply, My work flow: After getting raw data from Illumina Miseq. (Illumina Ampliseq kit was used ) (Source: genomic DNA) reference genome used: hg19 (I used samtool pipeline) 1st step: Mapping was done by using BWA mem 2nd step: Conversion of Sam to Bam file (using a fixmate command ...
written 8 months ago by rebecca0823810
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Comment: C: step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... ok, I will try again. Thanks! ...
written 8 months ago by rebecca0823810
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Comment: C: step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... I used above-mentioned command but still, it's not working. ...
written 8 months ago by rebecca0823810
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Comment: C: step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... Thank you so much for your reply! I tried mosdepth but it dint work. I used the following command: mosdepth -t 2 --by capture.bed $sample-output-prefix sample.exome.bam capture.bed (here I had given my Ampli designBed file and in exome.bam ( I had given my bam file) but this command is not worki ...
written 8 months ago by rebecca0823810
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Comment: C: step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... Thanks for your reply! Can you please suggest me pipeline for SNP analysis? Let me tell you in brief what I did after getting raw data from Illumina Miseq. reference genome used: hg19 1st step: Mapping was done by using BWA mem 2nd step: Conversion of Sam to Bam file (using a fixmate command) 3rd st ...
written 8 months ago by rebecca0823810
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step wise pipeline for SNP analysis (illumina Ampliseq sequencing)
... hello everyone! I am a beginner in data analysis... 1. Can anyone provide the pipeline for SNP analysis, please? (we used Illumina Ampliseq kit for library preparation) We used human DNA sample. 2. How we can calculate Illumina Ampliseq sequencing coverage? Thank you. ...
sequencing written 8 months ago by rebecca0823810 • updated 8 months ago by jackyen0

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