User: rmf
rmf • 340
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Posts by rmf
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Comment:
C: Raw counts to TPM in R
... Cool! I get the same result.
# michael's version
# https://support.bioconductor.org/p/91218/
tpm3 <- function(counts,len) {
x <- counts/len
return(t(t(x)*1e6/colSums(x)))
}
Michael's version is much faster despite all the transposes.
![enter image description h ...
6
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... Can someone verify if this R code for converting raw counts to TPM is correct?
#' @title Compute TPM for a read count matrix
#' @param dfr A numeric data.frame of read counts with samples (columns) and genes (rows).
#' @param len A vector of gene cds length equal to number of rows of df ...
written 25 days ago by
rmf • 340
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... Probably because there are very little gaps in alignments. Also I suppose the mash distance could be improved by setting a better value for the kmer length. I used 12 arbitrarily. ...
written 7 weeks ago by
rmf • 340
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... Oh. I wasn't aware of that. Good to know. Thx! ...
written 7 weeks ago by
rmf • 340
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... @genomax I used emboss `needle` as the final solution which is why I accepted that as the answer. ...
written 7 weeks ago by
rmf • 340
3
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... Comparing pairwise similarity measures between ~3000 fasta pairs in the size range 0-10000 nt.
**blast_identity**: Percentage identity as returned by BLASTN
blastn -query query.fa -subject ref.fa -task blastn -outfmt "6 pident nident"
**nw_identity**: Percentage identity as returned by need ...
written 7 weeks ago by
rmf • 340
0
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... They are comparable in lengths. The length difference range from 0 to 83 nt. ...
written 7 weeks ago by
rmf • 340
0
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... I am comparing human X and Y chromosomes. Y is rearranged and jumbled up. But I have already identified short regions in X that correspond with Y. Now I just need to figure out how similar they are. Here is an example
>chrX:153598967-153599086
TCCATGATGAACCTCGCCACTCGGAAGTGCACCCTGGCTTCGGG ...
written 7 weeks ago by
rmf • 340
0
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... Ah yes! Good point. But, does local matter for short sequences of few hundred nucleotides? ...
written 7 weeks ago by
rmf • 340
0
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... I haven't tried all the suggestions here, but I came across this BLAST usage:
blastn -query "query.fa" -subject "ref.fa" -task "blastn" -outfmt 6 >> blast_results.txt
And this returns
query ref per_ident aln_len mismatch gapopen qstart qend sstart send evalue bitscore
...
written 7 weeks ago by
rmf • 340
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