User: badribio

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Posts by badribio

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Comment: C: deseq2 pre filter rna seq
... excuse me, hope i did ok this time. ...
written 13 days ago by badribio0
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deseq2 pre filter rna seq
... I see more and more papers these days that use a read cut off before deseq2 analysis, I wonder what is the rational and/or how do they arrive at how many reads is a right number..for example from one of the papers ```DESeq2 was applied to genes having more than 20 reads in half the number of samples ...
rnaseq deseq2 written 13 days ago by badribio0 • updated 13 days ago by zefrieira0
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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 23 months 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 23 months ago by badribio0 • updated 23 months ago by Michael Love24k
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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 2.1 years 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 2.1 years 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 2.1 years ago by badribio0 • updated 2.1 years ago by Michael Love24k
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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 2.3 years 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 2.3 years 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 2.3 years ago by badribio0

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