User: boczniak767

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boczniak767600
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Posts by boczniak767

<prev • 124 results • page 1 of 13 • next >
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Comment: C: Small pathways but big network files
... Thanks for reply, I use version 3.5 in work and 3.6.1 on my laptop. ...
written 8 days ago by boczniak767600
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Small pathways but big network files
... 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? ...
network cytoscape written 10 days ago by boczniak767600 • updated 8 days ago by scooter50
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Answer: A: How To Get Consensus Sequence Including Variant From A Vcf File For Several Indi
... 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 7 months ago by boczniak767600
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Comment: C: bedtools coverage gives error received illegal bin number, but that number isn't
... I have the same error, it turns out that my bed file has positions reversed. So start coordinate was higher than stop. ...
written 10 months ago by boczniak767600
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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 13 months ago by boczniak767600
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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 13 months ago by boczniak767600
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Answer: A: How to extend bed intervals to a uniform size?
... You could also check very good one-liner solution provided in this message https://www.biostars.org/p/241744/ ...
written 13 months ago by boczniak767600
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Comment: C: Combining Microarray and RNAseq data
... I think, Probability Of Expression package could help https://rdrr.io/bioc/metaArray/man/poe.mcmc.html. ...
written 14 months ago by boczniak767600
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Comment: C: Probes - to - genes expression analysis question
... 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 14 months ago by boczniak767600
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Answer: A: Remove columns and rows which have only NAs without deleting all the data
... 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 14 months ago by boczniak767600

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