User: Daria

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Daria0
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Posts by Daria

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Comment: C: tx2gene for xenopus LAEVIS
... If I succeed to rename FASATA and re-do the alignment and get .sf files with normal names - GenBank IDs, how then I associate the data with OrgDb object? Would it come like this? k <- keys(z, keytype = "ACCNUM") tx2gene <- select(z, k, "ENTREZID", "ACCNUM") and then txi <- ...
written 7 weeks ago by Daria0
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Comment: C: tx2gene for xenopus LAEVIS
... And could you please clarify, if in principle it is possible for R to change FASTA names to GenBank IDs in .fasta files, why the same operation can't be made for the column "name" in .sf files and the alignment should be re-done? ...
written 7 weeks ago by Daria0
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Comment: C: tx2gene for xenopus LAEVIS
... ## replace FASTA names with just GenBank ID names(fastas) <- sapply(strsplit(names(fastas), "|"), "[", 4) ## write out FASTA with truncated names writeXStringSet(fastas, ) Strangely, this code changes all FASTA names to "1". ...
written 7 weeks ago by Daria0
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Comment: C: tx2gene for xenopus LAEVIS
... Thank you, James! ...
written 7 weeks ago by Daria0
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Comment: C: tx2gene for xenopus LAEVIS
... If I understand correctly tximport allows to import all .sf files from the experiment together and connect transcript IDs to gene IDs and join the counts for the same gene that come from different transcripts. To connect transcript IDs to geneIDs there should be tx2gene data frame that contains that ...
written 7 weeks ago by Daria0 • updated 7 weeks ago by James W. MacDonald51k
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Comment: C: tx2gene for xenopus LAEVIS
... Thank you very much for answer! I will try to perform it and get back. ...
written 7 weeks ago by Daria0
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tx2gene for xenopus LAEVIS
... I am working with xenopus LAEVIS. For alignment I used mRNA sequence from genebank. Is it possible to do tx2gene for this organism? it is absent here ftp://ftp.ebi.ac.uk/pub/databases/gencode/ and even here https://bioconductor.org/packages/release/bioc/manuals/AnnotationDbi/man/AnnotationDbi.pdf . ...
deseq2 written 7 weeks ago by Daria0 • updated 7 weeks ago by James W. MacDonald51k
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samples.txt?how to generate
... I have 3 control and 3 experiment samples and quant.sf files for all of them. I would like to run deseq, however I have no idea how to create samples.txt and can't figure it out from tximport documentation. ...
deseq2 written 7 weeks ago by Daria0 • updated 7 weeks ago by James W. MacDonald51k

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