[miso-users] error processing paired-end data

[Yarden Katz]

Hi Uma,

MISO does not support mixed read lengths, so that means you have to either trim your FASTQ files to a uniform read length and remap them (you can easily do the trimming with something like fastx-toolkit or similar tools), or trim the read lengths at BAM alignment.  The latter option is tricky as it can be unclear how to trim BAM alignments while preserving the CIGAR string (spliced alignment) information.  

Best, --Yarden


On Jan 28, 2014, at 11:56 AM, miso-users-owner at MIT.EDU wrote:

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>    Subject: error processing paired-end data
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> From: "Shankavaram, Uma (NIH/NCI) [E]" <uma at mail.nih.gov>
> Date: January 28, 2014 11:56:19 AM EST
> To: "'miso-users at mit.edu'" <miso-users at mit.edu>
> Subject: error processing paired-end data
> 
> 
> Hello,
> 
>  
> 
> I want to compare my samples at differential isoform expression. I am using sorted and indexed bam files and I am getting the following error:
> 
> Does this means, I have redo alignment with fixed read lengths? How do I do it? Or, this error means something else?
> 
> Did anyone got a similar issue?
> 
>  
> 
> Thanks for any help.
> 
>  
> 
> Uma
> 
>  
> 
> Loading settings from: /usr/local/Python/2.7.5/lib/python2.7/site-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt
> 
> Computing Psi values...
> 
>   - GFF index: /data/MISO
> 
>   - BAM: /data/bam/P01sorted.bam
> 
>   - Read length: 100
> 
>   - Output directory: /data/MISO/P01_miso
> 
> Checking your GFF annotation and BAM for mismatches...
> 
> Checking if BAM has mixed read lengths...
> 
>  
> 
> WARNING: Found mixed length reads in your BAM file! MISO does not support mixed read lengths. Please trim your reads to a uniform length and re-run or run MISO separately on each read length. Proceeding anyway, though it is likely that this will result in errors or inability to match reads to your annotation.
> 
>  
> 
>  
> 
> 
> 
> 
> From: miso-users-request at mit.edu
> Subject: confirm 8e453bb0c6449bc8a772db0ee88cf990d892e6db
> 
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