User: badribio

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Posts by badribio

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Comment: C: how to plot heatmap with in cell type comparison using contrasts.
... Thought so, was trying to push my luck here thank you ...
written 7 weeks ago by badribio0
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how to plot heatmap with in cell type comparison using contrasts.
... Previously i asked, this question https://support.bioconductor.org/p/96832/   Based on the response and some reading i used this design,    sample tissue sample1 tissue1 sample1 tissue1 sample2 ...
deseq2 written 8 weeks ago by badribio0 • updated 8 weeks ago by Michael Love14k
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Comment: C: deseq2 and dexseq for multiple tissue from wildtype only
... Thanks, is there a sample code that you would have come across in the past? It will help me understand better appreciate it! ...
written 4 months ago by badribio0
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Comment: C: deseq2 and dexseq for multiple tissue from wildtype only
... so if i understand it correct i can add group as a factor for the design something like this  tissue wild type group tissue1 group1 tissue1 group1 tissue1 group1 tissue2 group2 tissue2 group2 tissue2 group2 ...
written 4 months ago by badribio0
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deseq2 and dexseq for multiple tissue from wildtype only
... I have to analyze following experimental design  tissue wild type sequence library tissue1 paired-end tissue1 paired-end tissue1 paired-end tissue2 paired-end ...
rnaseq dexseq deseq2 written 4 months ago by badribio0 • updated 4 months ago by Michael Love14k
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Comment: C: DEXSeq Error in FUN(X[[i]], ...) : subscript out of bounds not sure why
... Snap shot of one of the sample, in igv ...
written 6 months ago by badribio0
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Comment: C: DEXSeq Error in FUN(X[[i]], ...) : subscript out of bounds not sure why
...  so if I am comprehending it correct although the function is DEXSeqDataSetFromHTSeq it still expects the input from dexseq_count.py?  If so then could you please let me know which file would the right result to use for downstream analysis based on my sequencing type? rna seq data paired end strand ...
written 6 months ago by badribio0
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Comment: C: DEXSeq Error in FUN(X[[i]], ...) : subscript out of bounds not sure why
... let me walk you through my steps may be you could please point out where i went wrong, 1) Bam files processed using Htseq count with parameters with parameters: --mode intersection-strict --minaqual 1 --stranded reverse --type exon --idattr gene_id using gtf (not gff) from mm9.37.67(ensembl)  2) l ...
written 6 months ago by badribio0
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DEXSeq Error in FUN(X[[i]], ...) : subscript out of bounds not sure why
... suppressPackageStartupMessages( library( "DEXSeq" ) ) setwd("pathto/htseq") inDir = getwd() countFiles = list.files(inDir, pattern = "htseq.txt$", full.names = TRUE) flattenedFile = ("pathto/ensembl/Mus_musculus.NCBIM37.67.gtf") mouseTable = data.frame(   row.names = c("S75","S76","S77","S72","S73" ...
dexseq written 6 months ago by badribio0
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Comment: C: DEXSeq unable to process Hisat2 bam
... I see thanks, so it should look like this SRR1910473.1 instead of SRR1910473.1.1 correct?   Could you please suggest any scripts to modify that are in line with DEXSeq structure and not mess the bam file. Thank you for prompt response.            ...
written 6 months ago by badribio0

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