User: raquelgarza95

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Posts by raquelgarza95

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(Closed) DESeq2: Continuous and discreate variables in the design
... Hello, I'm trying to get my head around some DESeq2 results and I would really appreciate some help. I have two conditions (control and disease) and one continuous variable (age). Each of the conditions would be conformed by 100 individuals with different ages. I want to see which changes occur ...
R deseq2 deseq rna-seq written 3 months ago by raquelgarza9550
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Representing several BAM files into one?
... Hello, I have four samples from the same condition (BAM files) and two controls (also BAM files). I want to eventually use plotHeatmap and plotProfile from deepTools, and I **dont** want to have six heatmaps sitting next to each other. I want the signal of the four samples to be represented as one ...
deeptools bam bamcompare written 5 months ago by raquelgarza9550
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Comment: C: Different mappings, different PCAs using TEtranscripts
... Thank you for your answer! ...
written 10 months ago by raquelgarza9550
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Comment: C: Different mappings, different PCAs using TEtranscripts
... Thank you for your answer. This is human data, and I am using the repeat information that TEtranscripts offer for other analysis. I was expecting similar results from the two approaches and was wondering if there was a reason behind it. Even if the software was not specifically designed to only wor ...
written 10 months ago by raquelgarza9550
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Comment: C: Different mappings, different PCAs using TEtranscripts
... The unique mapping is made with transcripts (79,000), TEtranscripts outputs gene read counts so it is less (24,333 genes). ...
written 10 months ago by raquelgarza9550
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Different mappings, different PCAs using TEtranscripts
... Hello, I made two PCA plots from two types of mappings towards the same genome. In one of them, I allow the reads to just map to one loci, and in the other one I let them map 100 times. After that I do transcript assembly with StringTie in the uniquely mapped reads, and i use the software TEtransc ...
tetranscripts pca written 10 months ago by raquelgarza9550
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Comment: C: StringTie strandness of library in dUTP protocol
... Your figures are very helpful, thank you. ...
written 10 months ago by raquelgarza9550
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StringTie strandness of library in dUTP protocol
... Can somebody explain to me why StringTie calls fr-firststrand to a library preparation that is prepared by dUTP protocol? dUTP protocol keeps the reverse strand of the amplified cDNA, right? So if it is the reverse strand, wouldn't it make more sense to call it secondstrand? Maybe the answer is "b ...
rnaseq libraryprep stringtie dutp written 10 months ago by raquelgarza9550 • updated 10 months ago by Juke-343.3k
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Comment: C: DESeq interactions: What genes that are different between two experiments affect
... Thank you! This was very helpful. ...
written 11 months ago by raquelgarza9550
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DESeq interactions: What genes that are different between two experiments affects the conditions
... Hello! I'm super noob on DESeq interactions so sorry in advance if this question is duplicated. I just need to ask directly to see if I understand correctly. I have two experiments performed in young and old mice. I want to test in both for knock down vs control of a certain gene. I want to make ...
dea interactions deseq2 rna-seq written 11 months ago by raquelgarza9550 • updated 11 months ago by swbarnes27.5k

Latest awards to raquelgarza95

Popular Question 6 months ago, created a question with more than 1,000 views. For From BAM to BAI to BIGWIG
Student 11 months ago, asked a question with at least 3 up-votes. For StringTie giving different results - same dataset

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