Question: randomreads.sh simulated reads dont map to genome
0
gravatar for grant.hovhannisyan
11 months ago by
grant.hovhannisyan1.6k wrote:

I have simulated "error-free" reads from the transcriptome using randomreads.sh from BBMap suit, but when I map them back to the genome using STAR I get just 88% of unique mapping, and around 11% of unmapped reads.

The command for simulation is

randomreads.sh \
ref=cglab_transcriptome.fa \
out1=reads1.fastq \
build=1 \
length=100 \
reads=500000 \
replacenoref=t \
simplenames=t \
seed=-1 \
paired=f \
metagenome=f \
addpairnum=t \
snprate=0 \
midq=35 \
maxq=39 \
minq=30 \
maxsnps=0 \
maxinss=0 \
maxdels=0 \
maxsubs=0 \
maxns=0

So I assume that it should produce ideal reads without snps/snvs. However, I see that its not the case when I align the non mapped read against the corresponding transcript.

Any suggestions what's going on? Do I miss any parameter of randomreads.sh ?

bbmap • 289 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by grant.hovhannisyan1.6k

You're simulating based on the transcriptome and aligning it back to the genome, right? Maybe the two references don't share a 100% overlap?

ADD REPLYlink written 11 months ago by RamRS22k

Good point, but I get the transcriptome from the genome using gffread.

ADD REPLYlink written 11 months ago by grant.hovhannisyan1.6k

All aligners have some fuzziness built into them. They all depend on an initial match that gets extended out.

Have you tried to use bbmap.sh to align the reads? Some of them could also be multi-mapping and depending on how many STAR reports by default some alignments may get left out.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax68k

Re multimappings, so I wouldn't have been surprised to see mulitmappers, but they constitute to just <1%. 10% are not mapped because of short alignments (in STAR terminology). And I don't have experience with BBmap to be honest. Is it comparable with STAR in sense of speed and accuracy?

ADD REPLYlink written 11 months ago by grant.hovhannisyan1.6k

Proof is in the pudding. Try it out yourself :-)

ADD REPLYlink written 11 months ago by genomax68k

indeed, but old friends and old wine are the best:)

ADD REPLYlink written 11 months ago by grant.hovhannisyan1.6k

Try bbmap.sh out. You would not regret it.

ADD REPLYlink written 11 months ago by genomax68k
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