User: simplitia

gravatar for simplitia
simplitia20
Reputation:
20
Status:
New User
Location:
Last seen:
4 months ago
Joined:
2 years, 2 months ago
Email:
s********@gmail.com

Posts by simplitia

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
165
views
1
answer
How to deconvolute whole blood and analyzed cell type separately for EWAS
... Hi I have whole blood CpG from the 850K EPIC plateform. My goal is to try understand how deconvolusion works; that is would it be possible separate out the cpgs into different subtype and run a EWAS for each cell type. separately? For example lets say I'm comparing group A to control using whole ...
epic methylation 850k cpg written 4 months ago by simplitia20 • updated 4 months ago by Kevin Blighe21k
0
votes
8
answers
65k
views
8
answers
Comment: A: How to download raw sequence data from GEO/SRA
... Hi, how do we put in a dbgap crendentials? I tried: prefetch -v SRR617345 but I'm getting this error. err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR617345' - Access denied - please request permission to access phs000468/PCR in d ...
written 4 months ago by simplitia20
1
vote
1
answer
297
views
1
answers
Comment: C: How to quantify PCR duplication from bam file
... After searching around a bit the solution is to use samtools flagstat; this works for me in case someone else stumbles on to this thread. thanks. ...
written 5 months ago by simplitia20
1
vote
1
answer
297
views
1
answer
How to quantify PCR duplication from bam file
... Hi I know that I can mark and remove duplicate using picard. However is there way I can quantify how much duplication I have? So for example lets say I have file1.bam - mark and remove duplication resulting in file2.bam now what I like to do is quantify pcr duplication for file1.bam and file2.b ...
rna-seq written 5 months ago by simplitia20 • updated 5 months ago by genomax49k
0
votes
0
answers
355
views
0
answers
Comment: C: Hard time trying to calculate Allele Frequency and DP from Platypus
... yes its good to check, I think you mean NF + NR = TR ; thanks again, super helpful. ...
written 5 months ago by simplitia20
1
vote
0
answers
355
views
0
answers
Comment: C: Hard time trying to calculate Allele Frequency and DP from Platypus
... @Kevin Blighe: yes thank you I'm still new to handling VCF files and your question was enough to answer my question since the header already contained the info I needed which was defining what each of those mean. For allele frequency I think this would be TR / TC since the header reads INFO=I ...
written 5 months ago by simplitia20 • updated 5 months ago by Kevin Blighe21k
2
votes
0
answers
355
views
0
answers
Hard time trying to calculate Allele Frequency and DP from Platypus
... Hi I'm using Platypus for variant calling, but I'm having a hard time understanding the INFO header, most of which I cannot find in VCFv4.1 - ultimately what I'm trying to extract is DP and AF, however the header just does not make any sense to me nor can I find it in google. For example from the h ...
snv rna-seq written 5 months ago by simplitia20 • updated 5 months ago by genomax49k
0
votes
0
answers
376
views
0
answers
Comment: C: Help with BWA: how to align paired as single and then combine again
... Thanks. This is going to be more complicated than I expected. I will try your method out first since its the most straightforward. I will post back here on an update. ...
written 6 months ago by simplitia20
0
votes
0
answers
376
views
0
answers
Comment: C: Help with BWA: how to align paired as single and then combine again
... thanks this looks good. One worry I have is would the merge bam still contain duplicate header info? If that is the case other tools from picard like MarkDuplicates is going to crash with the same error. ...
written 6 months ago by simplitia20
0
votes
0
answers
376
views
0
answers
Comment: C: Help with BWA: how to align paired as single and then combine again
... I have the same question so I'm bit at odd but I'm sure the authors had a good reason. Its from a paper and here is the github: https://github.com/rpiskol/SNPiR ...
written 6 months ago by simplitia20

Latest awards to simplitia

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: 1704 users visited in the last hour