User: sakura.nussbaum

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Posts by sakura.nussbaum

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Comment: C: Error in strsplit() : non-character argument - using DEXSeq
... Hi Alejandro, Indeed, I have around 10mio per library. So it seems ok! Thank you again, Sakura ...
written 3.6 years ago by sakura.nussbaum10
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Comment: C: Error in strsplit() : non-character argument - using DEXSeq
... Thank you for your answer! It was indeed (one of) the problem(s). I put -s reverse and now I have 1 million empty counts. However, it still seems high. Do you think it can come from somewhere else? Best, Sakura   ...
written 3.6 years ago by sakura.nussbaum10
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Comment: C: Error in strsplit() : non-character argument - using DEXSeq
... Hello, Thanks for the reply, I reinstalled DEXSeq and indeed obtained the same error, as it happened to me a few days ago. At this point I had tried to follow the advices given here: https://support.bioconductor.org/p/46484/ and this started to give me empty files. But now that I tried again, it se ...
written 3.6 years ago by sakura.nussbaum10
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Comment: C: Error in strsplit() : non-character argument - using DEXSeq
... Here it is: https://www.dropbox.com/s/m2zhchpc6vf5nmo/mm10.genes.gtf?dl=0 ...
written 3.6 years ago by sakura.nussbaum10
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dexseq_prepare_annotation gives an empty gff file
... Hello, I am trying to follow this pipeline and I have problems preparing the gtf file. I enter the following command:   python /Library/Frameworks/R.framework/Versions/3.2/Resources/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py mm10.genes.gtf mm10.genes.gff But it keeps giving me ...
dexseq prepare annotation empty gff written 3.6 years ago by sakura.nussbaum10
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Comment: C: Error in strsplit() : non-character argument - using DEXSeq
... Yes, sorry you are right, this was a gff file that I obtained previously by converting the gtf.  So I realised the problem happened when preprocessing the gtf. Here are the 10 first lines of gtf file: chr1    unknown    exon    3214482    3216968    .    -    .    gene_id "Xkr4"; gene_name "Xkr4" ...
written 3.6 years ago by sakura.nussbaum10
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Comment: C: Error in strsplit() : non-character argument - using DEXSeq
... Hello, of course, here they are:   chr1    unknown    gene    3214482    3671498    .    -    .    ID=Xkr4;Name=NM_001011874 chr1    unknown    exon    3214482    3216968    .    -    .    Parent=Xkr4 chr1    unknown    stop_codon    3216022    3216024    .    -    .    Parent=Xkr4 chr1    unknown ...
written 3.6 years ago by sakura.nussbaum10
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Error in strsplit() : non-character argument - using DEXSeq
... Dear all, I am a new user of DEXSeq and I would need some help concerning an error message that I get.   When I call the DEXSeqDataSetFromHTSeq, I obtain the following error: > library(DEXSeq) > dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= ~ sample + exon + con ...
dexseq dexseq_count dexseqdatasetfromhtseq strsplit written 3.6 years ago by sakura.nussbaum10 • updated 3.6 years ago by aditi20
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Comment: C: Error: could not find function "HTSeqCounts"
... Thank you all for your answers. I changed the method and I am now following this pipeline as you suggested. However, I also have some problems. When I call the DEXSeqDataSetFromHTSeq, I obtain the following error: > dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= ~ sam ...
written 3.6 years ago by sakura.nussbaum10
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Comment: C: Error: could not find function "HTSeqCounts"
... I realised that I had an error, I was supposed to type "read.HTSeqCounts()" instead of just "HTSeqCounts()", but id did not solve my problem, I still get: Error: could not find function "read.HTSeqCounts" I am trying to follow the pipeline from this source, and it seems that this function is in th ...
written 3.6 years ago by sakura.nussbaum10

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For Error in strsplit() : non-character argument - using DEXSeq

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