User: maria2019
maria2019 • 10
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Posts by maria2019
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... Did you get ~160k-180k variants with your WES analysis? Now I get confused. I get 130K variations for only exome region and 400K including exomes, UTRs, and intron!
However, the above comments mention that it should be ~ 30K-40K for exomes. So is 30K normal or 160K that you mentioned? ...
written 20 days ago by
maria2019 • 10
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... Thank you very much. your comments are very helpful ...
written 20 days ago by
maria2019 • 10
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... Thank you very much Emiliy. This was SO helpful. ...
written 20 days ago by
maria2019 • 10
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... I have WES/WGS data on a normal embryonic stem cell line and I want to cell any possible variants in it. I worked with the GATK germline variation calling and I got the results that I should've gotten if I had a germ cell.
Is that normal? Can you use germline variation calling on a normal embryonic ...
written 21 days ago by
maria2019 • 10
• updated
20 days ago by
Emily_Ensembl ♦ 18k
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Comment:
C: DNAseq pipeline steps
... I am very new in WGS, WES analysis. I was wondering if this workflow that you mentioned worked for you? ...
written 21 days ago by
maria2019 • 10
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... I used qualimap 2 times. Once I only used hg38 without a bed file. Then I used a bed file that I got from genome browser table:
(http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doMainPage=Back) and chose exons option for the output as a bed file. Is that what you mean? Or I will have to create my own ...
written 22 days ago by
maria2019 • 10
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... Hi, thanks for your response. Below are the commands I used:
1. Trimming with cutadapt reports:
Encoding: **Sanger . Illumina 1.9**, Tot sequences: 56558516, GC%: 49%
2. alignment:
**2.1. bwamem:**
$ bwa index genome.fasta genome
$ bwa mem -M -t 70 hg38.fa trimmed.R1.fastq trimmed.R2.fastq | sam ...
written 22 days ago by
maria2019 • 10
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... I want to do WGS and WES alignment with BWA mem. Should I use the same reference indexing command for both WES and WGS?
I know that reference indexing for WGS would be: "bwa index -a bwtsw ref.fa"
- Should I use the command for the WES or I should remove the **- a bwtsw** and go with "bwa index ...
written 23 days ago by
maria2019 • 10
• updated
23 days ago by
finswimmer ♦ 11k
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... Thank you for your answer. I have tried both ways and then I see a good fastQC result with either of them! That is why I am not sure if I should just keep the first one or dig into it and find out which one is better.
What would be the good comparison point to decide which one to use? ...
written 23 days ago by
maria2019 • 10
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How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?
... I have a **normal** human embryonic stem cell line (hESC) and the WES data analysis gives me 109313 SNP and 9943 Indel results. Are these numbers normal for a NORMAL cell line? I was thinking since this is a normal cell line it should not have many SNPs.
For the SNP calling I used samtools and I did ...
written 23 days ago by
maria2019 • 10
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