User: Lisa

gravatar for Lisa
Lisa310
Reputation:
310
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Location:
Ireland
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6 hours ago
Joined:
7 years, 3 months ago
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l*********@gmail.com

Posts by Lisa

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Time-course RNA-seq analysis in Deseq2
... Yeah, I am redoing it the way you have suggested now. Sorry if I was unclear. I meant that I subsetted the data into t0.vs.t3, t1.vs.t3, and t2.vs.t3, ran feature counts on them all individually and then did the deseq2 on each subset. I see now that this was unnecessary. Thanks for clarifying ...
written 25 days ago by Lisa310
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Comment: C: Time-course RNA-seq analysis in Deseq2
... Thank you for the links to the literature, I will have a read and see what else I can use to answer my questions. At the moment, the differential gene expression seems the most appropriate choice, as the ultimate ideal goal is to potential find biomarkers indicative of “disease” and “cure”. Howev ...
written 25 days ago by Lisa310
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Comment: C: Time-course RNA-seq analysis in Deseq2
... Hi Kevin, I actually did the pairwise comparisons separately, using a featureCounts matrix of just the two time-points in each comparison. Is it better practice to do them together? When you suggest an ANOVA between time-points do you mean for me to test the variance between the groups to test ...
written 25 days ago by Lisa310
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Time-course RNA-seq analysis in Deseq2
... Hi, I am looking to do a time-course analysis of my RNA-seq human, whole blood datasets. I have 30 samples, across 4 time-points. I have no replicates. T0 - Week 0, initial treatment T1 - Week 2, two weeks into treatment T2 - Week 12, twelve weeks into treatment T3 - Week 26, end of treatment; ...
R rna-seq written 26 days ago by Lisa310 • updated 26 days ago by Vitis1.6k
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Fold coverage in simulated reads not what it says it is?
... Hi,   I'm having a problem which I'm having difficultly pinpointing so sorry if I'm not being too clear.      I generated simulated reads using Art at different read lengths and fold coverage.  I'll include an example of the command line I used to make sure that I did that step correctly.  I generat ...
art assembly reads software error quake written 4.4 years ago by Lisa310
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Comment: C: How To Extract The Core Genes From The Orthomcl Output File?
... Thanks that makes a bit more sense. It seems really simple when you say it like that, so I think I was just having temporary brain melt or something. ...
written 4.7 years ago by Lisa310
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How To Extract The Core Genes From The Orthomcl Output File?
... Hi. I was wondering if anybody can help me figure out how to use Orthomcl to identify the core genome of E. coli genomes? I have 52 E. coli genomes that I used in orthomcl to produce ortholog groups. I followed all the steps in the user guide, until I got to the end. Now I'm left with this massi ...
orthomcl written 4.7 years ago by Lisa310 • updated 4.2 years ago by amanjain0
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Comment: C: How To Determine The Core Genome From The Orthomcl Output
... Deadly thanks. I shall do that. And provide as many details as I can. ...
written 4.7 years ago by Lisa310
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Comment: C: How To Determine The Core Genome From The Orthomcl Output
... Hi. Sorry for digging up an old post. I was just wondering has anybody solved this? I was wondering the same thing and wasn't sure if I should post a new question when this ones exists. ...
written 4.7 years ago by Lisa310
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Comment: C: Orthomcl Incompatibility With Mysql5.5.20
... I also recently had the same problem and found that this connect string worked for me, as some of the others suggested just wouldn't work for me for some reason. : dbConnectString=dbi:mysql:orthomcl:mysql_local_infile=1:localhost:3306 ...
written 4.8 years ago by Lisa310

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Appreciated 23 months ago, created a post with more than 5 votes. For How To Extract The Core Genes From The Orthomcl Output File?
Popular Question 23 months ago, created a question with more than 1,000 views. For Fold coverage in simulated reads not what it says it is?
Popular Question 23 months ago, created a question with more than 1,000 views. For Mrbayes Mpi Version Not Working Correctly On Server
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Fold coverage in simulated reads not what it says it is?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Is Tophat The Only Mapper To Consider For Rna-Seq Data?
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