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[wgs-assembler-users] S. purpuratus parameters
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From: mathog <ma...@ca...> - 2015-01-20 20:37:18
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(This is a followup to: Re: [wgs-assembler-users] mer, mertrim running
single threaded on large SMP machine)
On 19-Jan-2015 18:52, Brian Walenz wrote:
> I didn't poke through the data much, just enough to see it was
> Illumina.
> My immediate reaction is to suggest trying masurca. It handles
> illumina
> much much better than plain CA, but does probably require more reads
> because more crap gets filtered out.
Will look into that. Also found Meraculous, also for Illumina. (So
many assemblers, so little time...)
> With your current assembly, I see two things I don't like: 1) bog
> instead
> of bogart, 2) 3% error rate.
>
>
> You can do some experiments with the current assembly without too much
> pain. All we're going to do is run bogart a few times, and look at the
> resulting unitigs. No consensus generation, just unitig layouts.
>
> On a COPY of the gkpStore, run
>
> gatekeeper --revertclear OBTCHIMERA *gkpStore
Did this:
cp -r ..gkpStore copygkpStore
cp ..gkpStore.err copygkpStore.err
cp ..gkpStore.errorLog copygkpStore.errorLog
cp ..gkpStore.fastqUIDmap copygkpStore.fastqUIDmap
cp ..gkpStore.info copygkpStore.info
export PATH=$PATH:/home/wgs_project/wgs/Linux-amd64/bin
#
gatekeeper --revertclear OBTCHIMERA copygkpStore
>
> This will restore the clear ranges to the state they had just after
> trimming, and just before unitigging.
>
> Then a bunch of iterations of bogart:
>
> bogart -G *.gkpStore -O *.ovlStore -T e10.tigStore -o test.bogart -eg
> 0.10
> -Eg 2.5 -em 0.10 -Em 2.5
>
> Where the eg and em parameter is varied between 2 and 6 (percent
> error).
> By default, overlaps are generated to only 6% error, not that higher
> would
> be feasible with short reads. The Eg and Em parameters measure overlap
> error as 'number of errors', to get around the problem of a 50-base
> overlap
> with one error resulting in 2% error. You can mostly ignore this for
> the
> higher error rates.
Sorry, the wild card in that line is throwing me. Also I'm confused if
you mean big Eg,Em (where 2.5 is in the range specified) or little eg,em
(where values are not in that range). Given what I called the copy, is
this what you want to run?
VAL=2.5 #2.5 percent
bogart -G copygkpStore -O copyovlStore -T e10.tigStore -o test.bogart \
-eg 0.10 -Eg $VAL -em 0.10 -Em $VAL
tigStore -g copygkpStore -t e10.tigStore 1 -U -d sizes -s 800000000
VAL=3.0 #3.0 percent
bogart -G copygkpStore -O copyovlStore -T e10.tigStore -o test.bogart \
-eg 0.10 -Eg $VAL -em 0.10 -Em $VAL
tigStore -g copygkpStore -t e10.tigStore 1 -U -d sizes -s 800000000
# etc.
The bogart command fails because "'copyovlStore' is not an
ovelrapStore".
Use the overlapStore from the first run in that command?
(note the typo in the error message, that's what it says)
Erase the e10.tigStore between runs?
Do something to the overlapStore between runs?
running tigStore on the original (not so useful) run gave this:
tigStore -g ..gkpStore -t ..tigStore 1 -U -d sizes -s copygkpStore.info
utgLenUnassigned n10 siz 528 sum 304316578 idx 479977
utgLenUnassigned n20 siz 400 sum 608633078 idx 1148939
utgLenUnassigned n30 siz 291 sum 912949618 idx 2026098
utgLenUnassigned n40 siz 179 sum 1217266213 idx 3353557
utgLenUnassigned n50 siz 150 sum 1521582630 idx 5307416
utgLenUnassigned n60 siz 145 sum 1825899170 idx 7367619
utgLenUnassigned n70 siz 126 sum 2130215760 idx 9584603
utgLenUnassigned n80 siz 122 sum 2434532234 idx 12033900
utgLenUnassigned n90 siz 102 sum 2738848751 idx 14689647
utgLenUnassigned sum 3043165239 (genomeSize 0)
utgLenUnassigned num 18384123
utgLenUnassigned ave 165
tigLenSingleton n10 siz 150 sum 142617831 idx 907450
tigLenSingleton n20 siz 148 sum 285235697 idx 1865321
tigLenSingleton n30 siz 145 sum 427853436 idx 2837943
tigLenSingleton n40 siz 134 sum 570471289 idx 3850926
tigLenSingleton n50 siz 125 sum 713089018 idx 4969720
tigLenSingleton n60 siz 123 sum 855706883 idx 6116341
tigLenSingleton n70 siz 121 sum 998324590 idx 7282617
tigLenSingleton n80 siz 108 sum 1140942414 idx 8518814
tigLenSingleton n90 siz 87 sum 1283560221 idx 9981733
tigLenSingleton sum 1426177984 (genomeSize 0)
tigLenSingleton num 11893391
tigLenSingleton ave 119
tigLenAssembled n10 siz 630 sum 161699171 idx 231237
tigLenAssembled n20 siz 517 sum 323397821 idx 516513
tigLenAssembled n30 siz 443 sum 485096301 idx 855316
tigLenAssembled n40 siz 389 sum 646795227 idx 1245703
tigLenAssembled n50 siz 335 sum 808493956 idx 1690952
tigLenAssembled n60 siz 266 sum 970192570 idx 2232349
tigLenAssembled n70 siz 205 sum 1131891234 idx 2921817
tigLenAssembled n80 siz 157 sum 1293589836 idx 3836637
tigLenAssembled n90 siz 136 sum 1455288608 idx 4933675
tigLenAssembled sum 1616987255 (genomeSize 0)
tigLenAssembled num 6490732
tigLenAssembled ave 249
Presumably we want to see many more of the tigLenAssembled and fewer of
the utgLenUnassigned and tigLenSingleton.
Thanks,
David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech
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