User: boczniak767
boczniak767 • 600
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Posts by boczniak767
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... Late answer but maybe will be helpful for someone. This generates sequence for one indyvidual at a time.
First compress your `vcf` file
`bgzip name.vcf > name.vcf.gz`
Then make an index (requred by `vcf-consensus`)
`tabix name.vcf.gz`
Finally for SC9 individual
`cat reference_genome.fa | v ...
written 4 months ago by
boczniak767 • 600
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... I have the same error, it turns out that my bed file has positions reversed. So start coordinate was higher than stop. ...
written 7 months ago by
boczniak767 • 600
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Comment:
C: Convertion Of Gff3 To Gtf
... `gffread` from Cufflinks version 2.2.1 not work properly, it leaves only "gene_id" and "transcript_id" from the 9th column. E.g. exon number was stripped. I've not used the latest version, because I couldn't find the binaries and don't want to install additional packages needed for compilation. ...
written 10 months ago by
boczniak767 • 600
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Comment:
C: Convertion Of Gff3 To Gtf
... I'm not sure if this produce really **gtf**, after above commands I have "gff-version 2" in the header of exported file. ...
written 10 months ago by
boczniak767 • 600
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... You could also check very good one-liner solution provided in this message https://www.biostars.org/p/241744/ ...
written 10 months ago by
boczniak767 • 600
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... I think, Probability Of Expression package could help https://rdrr.io/bioc/metaArray/man/poe.mcmc.html. ...
written 10 months ago by
boczniak767 • 600
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... Probe-level analysis allows you to use it later, in case your probe-gene annotation improves.
> you could use the probes as variables in your analysis although you would probably still have to deal with the high correlation between probes targeting the same transcripts.
Its true, but it also al ...
written 10 months ago by
boczniak767 • 600
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... So, for a matrix `x` containing some rows and columns with all NAs try:
`x_no_na_col=x[,apply(!is.na(x),2,any)]` for columns
and
`ind <- apply(x_no_na_col, 1, function(x_no_na_col) all( is.na(x_no_na_col)))`
then
`x_no_na=x_no_na_col[!ind,]` for rows ...
written 10 months ago by
boczniak767 • 600
1
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... I suggest adding the commands you've tried. For columns confront [link][1] and for rows [link][2]
In fact it was not so hard to find ;-)
[1]: https://stackoverflow.com/questions/15752343/how-to-omit-columns-containing-only-nas-in-a-matrix
[2]: https://stackoverflow.com/questions/6471689/remove ...
written 10 months ago by
boczniak767 • 600
1
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2
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399
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2
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... I agree, there you could use DyNet app (http://apps.cytoscape.org/apps/dynet) ...
written 10 months ago by
boczniak767 • 600
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