thegenemyers / phase-mers Goto Github PK

Ok so here are some examples

15906 3080264 c
15924 134873123 %
15963 79233114 g
16082 92274759 %
16103 236847240 t
16105 266141784 a
16123 115277944 g
16143 113246232 a
16160 30081118 c
16246 13828099 %
16263 64421946 -
16264 262602883 s
16268 193003656 t
16281 2228246 -
16282 54067255 g
16284 219217962 :
16289 4784178 a
16293 220790910 -
16324 219217990 :

You said previously the - are the homozygous, so what are : and %?

The positions are of the start of the kmer?

how do you get two kmer pairs which are overlapping one another
16103 236847240 t
16105 266141784 a
?

and how do you get a homozygous kmer 1 base before a het pair
16263 64421946 -
16264 262602883 s
well presumably both of these signals could happen if the het pair actually came from paralogous sequence instead of heterozygosity. do you agree these are the only ways this could arise? OR I guess the hom kmer might not be a hom kmer in this last case. But the previous case i don't think i see how it could happen (2 overlapping het kmers).

Best,
Haynes

And after this i'll stop taking up your time. You have been very generous in all of this and of course we will include you in papers as this was done custom for me.

Hi Gene,

Sorry to bother you. I am trying to name everything and have it live in an output directory instead of just having everything have the same output prefix as the source data files.

so trying to unpack this

FastK -t? -p Foo               //  Build a table Foo.ktab and profile Foo.prof of HiFi data set Foo
Phasemer -m? Foo -NMers        //  Build tables Mers.U.ktab and Mers.L.ktab of het- and hom-mers
FastK -p:Mers.U Foo -NMap.U    //  Build relative profiles Map.U.prof of Foo w.r.t Mers.U
FastK -p:Mers.L Foo -NMap.L    //  Build relative profiles Map.L.prof of Foo w.r.t Mers.L
Phasemap -DFoo Map.U Map.L     //  Scan all profiles to output site locations in each read

First off, I'm getting the kmer spectra from short reads and applying it to long reads and linked reads and hic.

But okay so after the first line we have
Foo.bam (unaligned bam lets say)
Foo.ktab
Foo.prof

Then in the second line Phasemer uses just the Foo.ktab to find het and modimized homs and creates Mers.U and Mers.L.

Then FastK in the next two lines uses Foo.bam and Mers.U/L to create an upper bit or lower bit id profile for each read.

and then what I don't understand is in the final step, what all files need to be associated with -DFoo? Foo.prof, Foo.ktab, both? also Foo.bam? I am playing around with it but haven't figured it out yet.

Best,
Haynes

Hi， @richarddurbin @wheaton5 @thegenemyers

I can't compile Phasemap, beacause of some errors:

multiple definition of `Prog_Name'

my clang version is 14.0.6. What should I do?

my bad, i figured it out

.