User: tim.ivanov.92

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Posts by tim.ivanov.92

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Comment: C: visualizing alignment without realignment
... 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 7 months ago by tim.ivanov.920
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Comment: C: visualizing alignment without realignment
... 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 7 months ago by tim.ivanov.920
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Comment: C: visualizing alignment without realignment
... 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 7 months ago by tim.ivanov.920
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Comment: C: visualizing alignment without realignment
... 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 7 months ago by tim.ivanov.920
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visualizing alignment without realignment
... 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 ...
alignment visualization msa written 7 months ago by tim.ivanov.920 • updated 7 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Package for custom visualization of multiple sequence alignment
... 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 11 months ago by tim.ivanov.920
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Package for custom visualization of multiple sequence alignment
... 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 ...
visualization msa written 11 months ago by tim.ivanov.920 • updated 11 months ago by ulrich.bodenhofer20
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Comment: C: tximport's parameter for countsFromAbundance doesn't work
... 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 20 months ago by tim.ivanov.920
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Answer: A: tximport's parameter for countsFromAbundance doesn't work
... 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 20 months ago by tim.ivanov.920
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Comment: C: tximport's parameter for countsFromAbundance doesn't work
... > 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 20 months ago by tim.ivanov.920

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