User: as9309

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as930940
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4 years, 8 months ago
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Posts by as9309

<prev • 7 results • page 1 of 1 • next >
17
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Keeping pheatmap colour range the same for different data sets
... Hi, I've got fold change data for samples 1 and 2 from time point t1 to time point t2. I want to create a heat map using pheatmap for subsets of genes (~50-100 per set) but I want to be able to define the colour scale to be the same for all. At the moment, R picks the range based on the highest fo ...
R pheatmap rna-seq written 4.4 years ago by as930940 • updated 4.4 years ago by Selenocysteine600
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Comment: C: Cufflinks bias correction and DESEq2
... Hi, thanks - do you know if there is software on R to do this? I believe HTSeq-count requires python and featureCounts (rsubread) is only compatible with Mac? ...
written 4.6 years ago by as930940
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Cufflinks bias correction and DESEq2
... I ran all my RNA Seq data through galaxy to get FPKM files from original fastq data, but I did bias correction in Cufflinks. However, the DESeq2 manual stresses that you should use raw integer counts, not normalised counts. Does cufflinks normalise the data to some extent during bias correction? Sho ...
cufflinks deseq2 bias written 4.6 years ago by as930940 • updated 4.6 years ago by Nicolas Rosewick9.0k
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Comment: C: Using ensembl genomes and gtf conversion
... Yes, worked with the gff3 file! Thanks for your help. ...
written 4.7 years ago by as930940
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Comment: C: Using ensembl genomes and gtf conversion
... When I use cufflinks with the gff3 file, it provides the correct gene annotation but with incorrect gene names. e.g. instead of the RpoS gene, it gives me "transcript:AAC75783". Also, the cufflinks programme will not recognise my .tab file. Do you know how I can rearrange the gff3 file to identify t ...
written 4.7 years ago by as930940
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Comment: C: Using ensembl genomes and gtf conversion
... Thanks for your reply - yes I took the MG1655 genome from Ensembl bacteria but when I upload to galaxy, it recognises it as a gff file. ...
written 4.7 years ago by as930940
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Using ensembl genomes and gtf conversion
... Hi, I'm trying to align my RNA-seq data to an E coli reference genome that I downloaded from Ensembl bacteria but I'm getting stuck because I need the genome in gtf format. I can only download it in gff3 and cannot convert gff3 to gtf because gffread does not work ("Uncaught exception in exposed AP ...
genome rna-seq conversion gffread written 4.7 years ago by as930940 • updated 4.7 years ago by andrew.j.skelton736.0k

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