User: tim.ivanov.92
tim.ivanov.92 • 0
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Posts by tim.ivanov.92
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... also can you help me with dna alignments?
If i'm willing to realign with, for example muscle, i do it this way:
mySequences <- readDNAStringSet("100_slo_chr3R_24691930_24694960_1_exon2.fasta")
myFirstAlignment <- msa(mySequences,method = 'Muscle',type='dna')
msaPrettyPrint(myFirs ...
written 9 months ago by
tim.ivanov.92 • 0
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... ok, here is what i got
from
dflatex newaln.tex
> Admins-iMac:clusters_with_deletions timofei.ivanov$ pdflatex newaln.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./newaln.tex
LaTeX2e < ...
written 9 months ago by
tim.ivanov.92 • 0
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... no, sry - still this problem (also, i'm on mac, not windows)
newaln=as(AAMultipleAlignment("/Users/timofei.ivanov/projects/2bit_to_maf/clusters_with_deletions/74hephrevcompl.fasta"), "MsaAAMultipleAlignment")
> msaPrettyPrint(newaln, output="pdf", showNames="none",
+ s ...
written 9 months ago by
tim.ivanov.92 • 0
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... hm, it still doesn't work:
new_aln=as(AAMultipleAlignment("full_path_to_my_alignment.clw"), "MsaAAMultipleAlignment")
msaPrettyPrint(new_aln, output="pdf", showNames="none",
showLogo="none", askForOverwrite=FALSE, verbose=FALSE)
which result in error
> Error in texi2 ...
written 9 months ago by
tim.ivanov.92 • 0
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... I'm using [msa][1] package to visualize alignments which i already have.
But it seems that to create an msa object i can't use 'none' method
myFirstAlignment <- msa(mySequences,method = 'none')
> 'arg' should be one of “ClustalW”, “ClustalOmega”, “Muscle”
Is there a way to create an m ...
written 9 months ago by
tim.ivanov.92 • 0
• updated
9 months ago by
Martin Morgan ♦♦ 24k
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... thank you for the answer - this package looks quite all right, although i don't see in your example how can i actually access a single line in the alignment: it seems all i can do with this package is apply existing functions to regions inside an alignment, which is not quite my goal
...
written 13 months ago by
tim.ivanov.92 • 0
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... Is there a package to make custom visualization of multiple sequence alignments?
Specifically, i want to color some exons on a DNA alignment, knowing on their coordinates
...
written 13 months ago by
tim.ivanov.92 • 0
• updated
13 months ago by
ulrich.bodenhofer • 20
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... in case you wondering - tried updating tximport library and still got this error
> o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat))
Error in calcNormFactors.default(cts/normMat) : NA counts not permitted
and DEseq2 doesn't like this too:
> dds <- DESeqDataSetFr ...
written 22 months ago by
tim.ivanov.92 • 0
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... Also, can you help me on different issue with tximport?
I'm trying to get transcripts id's from *isoforms.results files, that look like this:
transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM Is ...
written 22 months ago by
tim.ivanov.92 • 0
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...
> which(is.na(txi.rsem$counts))
integer(0)
> which(is.na(txi.rsem$length))
integer(0)
...Which is weird, because i've found NaN values in workspace manually in the length matrix
...
written 22 months ago by
tim.ivanov.92 • 0
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