[miso-users] miso read-len parameter for pairedEnd reads with different lengths

[Yarden Katz]

Dear Sol,

I would recommend trimming read1 to 58bp, remapping, and passing MISO "--read-len 58".  If remapping is undesirable, then you can run just read1 as single-end like you suggested, but you'd lose the coverage from the other read mate, which if trimmed could also contribute to your single-end run.  Right now MISO does not support mixed read lengths, either within a pair or across pairs.

It's on my list to enforce more stringent error checking on this within MISO, to ensure that the --read-len parameter matches the BAM read length.

Best, --Yarden

On Dec 2, 2012, at 12:37 PM, Sol Katzman wrote:

> Dear Yarden,
> 
> I have pairedEnd Illumina data that I mapped with tophat. Due to a power outage,
> read2 was truncated, so that I have:
>  read1=75bp
>  read2=58bp
> 
> Since there is only a single (required) --read-len parameter for run_miso.py,
> is it possible to run miso (exon-centric analysis) on the tophat bams and get
> (reasonably) correct results?
> 
> If so, what should I use for --read-len?
> 
> If not, I will either
> a) just run miso with singleEnd (read1 only) bams
> b) trim the reads and re-map with tophat using 58x58bp
> 
> Thanks,
> /Sol.
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