User: skylinesky

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skylinesky10
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Posts by skylinesky

<prev • 5 results • page 1 of 1 • next >
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Flags in bam file and gene strand orientation
... Hello, I know that if a read has SAM flag 16 means that read has been mapped to the **reverse strand** in bam file. My question is: So does it mean that this read fall into the gene which is on **forward strand** in gene annotation files? (since gtf files are concerned with the coding sequences o ...
gene flag rna-seq orientation written 4 months ago by skylinesky10 • updated 4 months ago by Pierre Lindenbaum128k
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Comment: A: Clustering of DAVID gene enrichment results from gene expression studies
... Hello @kevin, Thank you for the code ! It is really helpful My question is every time I plot new dataset with this code, colors for the DEG sig score are keep changing. How can I fix the color of DEG significance color bar (as well as GO term score bar), Thanks in advance, ...
written 19 months ago by skylinesky10
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Comment: A: Gene expression analysis on gene counts from different genome builds
... Thank you for your answer, they are from same experiment, they just used two different genome builds to map reads. So I have mm9 and mm10 count files and want to analyse them together.. At first I thought even the genome annotation is different in half of the samples, overall result should be same. ...
written 22 months ago by skylinesky10
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Gene expression analysis on gene counts from different genome builds
... Hello all, I will do a differential gene expression analysis using Deseq2. However in my count data, half of the samples are aligned to reference genome using mm10 genome build, and the other half is aligned using mm9(bam files). I got their gene count data using their respective genome build. I ha ...
mm9 mm10 gene count deseq2 rna-seq written 22 months ago by skylinesky10
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mm9 gtf file gencode
... Hello , I am looking for mouse mm9 genome annotation file to use it in htseq count at the end. I decided to download it from gencode website(http://www.gencodegenes.org/mouse_releases/) On this website I downloaded m9 version. Does it correspond to ensembl mm9 build ? Actually at first I downloaded ...
gtf mm9 htseq count rna-seq written 2.4 years ago by skylinesky10 • updated 2.4 years ago by Kevin Blighe60k

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Popular Question 22 months ago, created a question with more than 1,000 views. For mm9 gtf file gencode

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