User: Sharon

gravatar for Sharon
Sharon120
Reputation:
120
Status:
Trusted
Location:
Last seen:
an hour ago
Joined:
6 months ago
Email:
s***********@gmail.com

Posts by Sharon

<prev • 112 results • page 1 of 12 • next >
0
votes
0
answers
25
views
0
answers
AD and heterozygotes in vcf
... Hello Every one When we have a variant with AD = 53, 50 for example or AD =800,80, does this just mean the variant is heterozygote, or it means we have low frequent variant since the reads that support the Alt is not higher than the ref ? How can I relate AD to heterozygosity? Thanks ...
vcf written 2 hours ago by Sharon120
0
votes
0
answers
96
views
0
answers
Comment: C: STAR reasonable parameters
... Thanks Devon and WouterDeCoster so much ! ...
written 8 days ago by Sharon120
0
votes
0
answers
62
views
0
answers
Comment: C: Some genes don't map to entrezID
... I used mapIds(org.Hs.eg.db) Here is a sample: symbol,logfc,adjpvalue HLA-DRB4,5.196415406,0.02376069902 SCGB1A1,4.269985245,0.01861663475 CST6,3.591334103,0.01391749469 CTCFL,3.455911002,0.01218323434 IGSF10,3.292159267,0.02287816294 DPYS,3 ...
written 8 days ago by Sharon120
0
votes
0
answers
96
views
0
answers
Comment: C: STAR reasonable parameters
... This is what I am already following, the reason for my question is what they say in the top of the pipeline: > "You should always make sure you understand what is being done at each > step and whether the values are appropriate for your data." ...
written 8 days ago by Sharon120
0
votes
0
answers
62
views
0
answers
Some genes don't map to entrezID
... Hi every one When some gene names fails to map to **entrez ID** when using GAGE and Kegg pathways, they are represented as NA. How can we fix this? Discarding them will remove too many genes that are important. When I try to map them myself, they usually have multiple names like this one (`GPR64 ...
kegg pathways gage written 8 days ago by Sharon120
0
votes
0
answers
96
views
0
answers
Comment: C: STAR reasonable parameters
... So how much to tamp down was my question, so you think default parameters of STAR is still fine and not aggressive? Thanks Devin so much ! ...
written 8 days ago by Sharon120
0
votes
0
answers
96
views
0
answers
Comment: C: STAR reasonable parameters
... I mean in variant calling. mismatches would be considered later as SNP? ...
written 8 days ago by Sharon120
0
votes
0
answers
96
views
0
answers
Comment: C: STAR reasonable parameters
... Like what? would salmon work with variant calling? And decreasing the alignment rate yes, but I don't want alignment with reads that has too many mismatches and softclipped, the default paramters are kinda high in this. What do you think? ...
written 8 days ago by Sharon120
5
votes
0
answers
96
views
5 follow
0
answers
STAR reasonable parameters
... Hi everyone I am using STAR for alignment with goal of variant calling, I feel the default parameters are too loosy, like too much mismatches, too much soft clipping, ..etc. I want to get some feedback from your experience about what are much reasonable parameters, it's my first use for STAR. Th ...
rna-seq written 8 days ago by Sharon120
0
votes
0
answers
82
views
0
answers
Comment: C: Tools for finding multiple or combinatorial mutations and variants?
... Ah, I appreciate if you can explain more the region conservation and comparable frequency. Like I compare the variant in case and control, keeping in mind possibly carrier, penetrance, ..etc. What else do you mean? Thanks ...
written 15 days ago by Sharon120

Latest awards to Sharon

Scholar 5 weeks ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Centurion 5 weeks ago, created 100 posts.
Scholar 5 weeks ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Scholar 7 weeks ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Scholar 8 weeks ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Scholar 8 weeks ago, created an answer that has been accepted. For A: Alignment dropped with Salmon
Supporter 9 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 839 users visited in the last hour