User: maria2019

gravatar for maria2019
maria201910
Reputation:
10
Status:
New User
Location:
Last seen:
2 days, 8 hours ago
Joined:
3 weeks, 3 days ago
Email:
h******@bgsu.edu

Posts by maria2019

<prev • 17 results • page 1 of 2 • next >
0
votes
2
answers
2.1k
views
2
answers
Comment: C: What is the expected rate of SNPs within a human exome sequencing with HiSeq?
... 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 maria201910
0
votes
1
answer
125
views
1
answers
Comment: C: why does qualimap2 shows different results for number of mismatches for bowtie2
... Thank you very much. your comments are very helpful ...
written 20 days ago by maria201910
0
votes
1
answer
122
views
1
answers
Comment: C: Can you use germline variation calling on a normal embryonic stem cell line?
... Thank you very much Emiliy. This was SO helpful. ...
written 20 days ago by maria201910
7
votes
1
answer
122
views
7 follow
1
answer
Can you use germline variation calling on a normal embryonic stem cell line?
... 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 ...
germline variation gatk wes snp embryonic cell written 21 days ago by maria201910 • updated 20 days ago by Emily_Ensembl18k
0
votes
0
answers
505
views
0
answers
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 maria201910
0
votes
1
answer
125
views
1
answers
Comment: C: why does qualimap2 shows different results for number of mismatches for bowtie2
... 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 maria201910
0
votes
1
answer
125
views
1
answers
Comment: C: why does qualimap2 shows different results for number of mismatches for bowtie2
... 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 maria201910
0
votes
1
answer
77
views
1
answer
Should I use the same reference indexing command of bwa for WGS and WES analysis?
... 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 ...
indexing wes bwa mem wgs written 23 days ago by maria201910 • updated 23 days ago by finswimmer11k
0
votes
1
answer
134
views
1
answers
Comment: C: What is the right illumina universal adapter sequence for trimming paired-end re
... 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 maria201910
0
votes
0
answers
95
views
0
answers
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 ...
wes samtools snp hesc written 23 days ago by maria201910

Latest awards to maria2019

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 890 users visited in the last hour