User: xd_d

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xd_d70
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Posts by xd_d

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Answer: A: Help understanding MACS2 --extsize and --shift
... Is the --extsize equal the window size ? ...
written 4 months ago by xd_d70
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MACS2 , pvalue
... Hello all, have some one an example how to calculate the p-value in MACS2 to call significante Peaks ? ...
sequence chip-seq written 4 months ago by xd_d70 • updated 4 months ago by Chris Fields1.8k
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Comment: C: RNAseq, Noise , Signal
... Everbody speak about noise or background noise, but nobody can explain that ? ...
written 5 months ago by xd_d70
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RNAseq, Noise , Signal
... Hello all, I have a question about noise in RNA-seq. What did that mean ? I dont finde a good answer on this question. ...
rna-seq noise written 5 months ago by xd_d70 • updated 5 months ago by Devon Ryan73k
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Comment: C: RNAseq, poly(A) selection
... From the human, RNAseq from brain tumor. I use a annotation from GENCODE v25. including protein coding genes and genes of lncRNA. I use the intron coodinates to search significant peaks on the introns. And I found many.. ...
written 5 months ago by xd_d70
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RNAseq, poly(A) selection
... Hello all, I have analyze some poly(A) RNAseq data. And I often see that a lot of reads are within intronic region. Has anybody an idea, what these annotated Elements are. Maybe SINE or LINE Elements ? ...
next-gen rna-seq sequencing written 5 months ago by xd_d70 • updated 5 months ago by Cacau390
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Aberrant Splicing, alternative splicing
... Hello all, I have read that many cancers have tumor specific alternative splicing isforms. When can I say that are aberrant splicing events. Is every different alternative splicing pattern from normal tissue a cause of aberrant splicing ? ...
rna-seq cancer written 5 months ago by xd_d70
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ncRNA, RNAseq, totalRNA, long ncRNA
... Hello all, my question is: can i analyze the expression of lncRNA and long lncRNA with total RNA seq data and RNAseq data with poly(A) selection ? Have anybody experience with that ? ...
rna-seq written 5 months ago by xd_d70 • updated 3 months ago by Biostar ♦♦ 20
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DEXseq alternative splicing detection
... Hello all, I know with DEXseq i get the differential usage of exon accross samples. I read in some papers that they detect 5'/3' alternative splicing events, but they dont say how they do that. Do anybody know how i get these events from a DEXseq workflow output ? ...
rna-seq written 5 months ago by xd_d70 • updated 5 months ago by kristoffer.vittingseerup350
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Comment: C: Alternative Splicing detection
... Hey thanks I read the paper: https://www.ncbi.nlm.nih.gov/pubmed/22266656 and they only test if a exon in a transcript or not. But i dont find alternative 5'/3' splicing sites. Do I need a 5' alternative splice annotation file for rMats ? ...
written 5 months ago by xd_d70

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