User: Bioinfo

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Bioinfo20
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Posts by Bioinfo

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Comment: C: Identifying differentially expressed lncRNA's from RNA-Seq data
... Ok but how can I detect differential expressed lncRnas if the gtf file is with pcRna and lncRnas? ...
written 3 days ago by Bioinfo20
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Comment: C: Identifying differentially expressed lncRNA's from RNA-Seq data
... Got it. Thankyou!! Could you also answer my second question which is mentioned above please. ...
written 3 days ago by Bioinfo20
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Comment: C: Identifying differentially expressed lncRNA's from RNA-Seq data
... You mean for hisat2 I need to create index files of Grch38 and the gtf file will be used for stringtie. Am I right ? How can I create index files? ...
written 3 days ago by Bioinfo20
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Comment: C: Identifying differentially expressed lncRNA's from RNA-Seq data
... No I am also looking for novel lncRnas. Just to know how the command should be given if I need to use gtf file with hisat2? ...
written 3 days ago by Bioinfo20
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Identifying differentially expressed lncRNA's from RNA-Seq data
... Hi I'm very new to this lncRNA things. I'm using HISAT2, STRINGTIE and BALLGOWN pipeline for differential expression analysis. If I'm only looking for lncRNA's, I will use the lncRNA annotation from Gencode lncRNA's [ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_24/gencode.v24.long_non ...
ngs rna-seq lncrna written 3 days ago by Bioinfo20 • updated 3 days ago by Devon Ryan73k
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How to cluster the annotation in the heat map?
... library(ComplexHeatmap) set.seed(123) mat = matrix(rnorm(100), 10) foo = sample(letters[1:2], 10, replace = TRUE) colnames(mat) = sapply(letters[1:10], function(x) paste(rep(x, 10), collapse = "")) cn = colnames(mat) ha2 = HeatmapAnnotation(foo = foo, ...
R clustering rna-seq heatmap written 9 weeks ago by Bioinfo20 • updated 9 weeks ago by Kevin Blighe8.9k
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Comment: C: RNA-seq cBioPortal differential gene expression
... Dear Tris, As mentioned above I have downloaded the TCGA data from cBioPortal. I would like to know about ‘data_RNA_Seq_v2_expression_median’. This have values like following: Hugo_Symbol TCGA-2V-A95S-01 TCGA-2Y-A9GS-01 TCGA-2Y-A9GT-01 UBE2Q2P3 1.5051 26.412 ...
written 3 months ago by Bioinfo20
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Comment: C: cuffmerge output question
... Nope I didn't have any fasta genome files with that. Is it compulsory to use fasta genome files for cuffmerge or index files are fine which are used for tophat? ...
written 6 months ago by Bioinfo20
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Comment: C: cuffmerge output question
... No, there are no genome fast files. I have only .bt2 files. How to generate genome fast file? ...
written 6 months ago by Bioinfo20
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Comment: C: cuffmerge output question
... Yes, I looked into it. It exists. I used the same for tophat also. Actually In b37 folder human_g1k_v37_decoy_bowtie2.1.bt2, human_g1k_v37_decoy_bowtie2.2.bt2, human_g1k_v37_decoy_bowtie2.3.bt2, human_g1k_v37_decoy_bowtie2.4.bt2, human_g1k_v37_decoy_bowtie2.rev.1.bt2, human_g1k_v37_decoy_bowtie2.rev ...
written 6 months ago by Bioinfo20

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