User: boczniak767
boczniak767 • 620
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Posts by boczniak767
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... Thanks for reply, I use version 3.5 in work and 3.6.1 on my laptop.
...
written 12 weeks ago by
boczniak767 • 620
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... Hi,
so I had a `cys` file with ca 10 big networks (ca 30k nodes each), giving a 100Mb file.
I decided to leave only three networks with max 30 (thirty) nodes to make file loading faster (much faster).
Nevertheless file size was reduced very little and the file loading takes very long.
Why is that? ...
written 12 weeks ago by
boczniak767 • 620
• updated
12 weeks ago by
scooter • 60
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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 9 months ago by
boczniak767 • 620
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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 12 months ago by
boczniak767 • 620
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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 16 months ago by
boczniak767 • 620
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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 16 months ago by
boczniak767 • 620
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... You could also check very good one-liner solution provided in this message https://www.biostars.org/p/241744/ ...
written 16 months ago by
boczniak767 • 620
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... I think, Probability Of Expression package could help https://rdrr.io/bioc/metaArray/man/poe.mcmc.html. ...
written 16 months ago by
boczniak767 • 620
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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 16 months ago by
boczniak767 • 620
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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 16 months ago by
boczniak767 • 620
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