Pairend_distro.py warning: only x elements

[Fabou13]

Hello, After running lumpy_smooth on a sample bam file I got the following warning message: Warning: only 392 elements in distribution (min: 1000) I figured out it comes from pairend_distro.py that does have enough elements to define mean and stdev. So it generates NA. I tried to run pairend_distro.py and tweaked the tail -n and the -N argument and got: Warning: only 413 elements in distribution (min: 1000) Do you have an idea what are the cause of that warning (coverage depth too low?)? What could I check to understand what's going wrong with thata sample? Does the min value of 1000 is the minimum acceptable or it can be lowered? Thanks in advance Fab

[ryanlayer]

Is the library normal paired end illumina sequencing?

On Dec 13, 2018, at 2:46 AM, Fabou13 notifications@github.com wrote:

Hello, After running lumpy_smooth on a sample bam file I got the following warning message: Warning: only 392 elements in distribution (min: 1000) I figured out it comes from pairend_distro.py that does have enough elements to define mean and stdev. So it generates NA. I tried to run pairend_distro.py and tweaked the tail -n and the -N argument and got: Warning: only 413 elements in distribution (min: 1000) Do you have an idea what are the cause of that warning (coverage depth too low?)? What could I check to understand what's going wrong with thata sample? Does the min value of 1000 is the minimum acceptable or it can be lowered? Thanks in advance Fab

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[Fabou13]

The library was made with NEBNext Ultra II Directional RNA. It is paired end illumina RNA-seq. I ran other samples from the same sequencing run with lumpy and they gave correct results.

[ryanlayer]

I have never used RNA in LUMPY, but I am going to guess you will get some pretty noisy results from all of the intron splicing. Your error indicated that it didn’t see enough normal reads to make a distribution. This may be why.

On Dec 13, 2018, at 5:24 AM, Fabou13 notifications@github.com wrote:

The library was made with NEBNext Ultra II Directional RNA. It is paired end illumina RNA-seq. I ran other samples from the same sequencing run with lumpy and they gave correct results.

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[Fabou13]

I am actually running lumpy on RNA viruses to detect recombinant genomes from two parental genomes. The output of SVtyper are fine for some samples and quite coherent. But I am having some samples for which I get the warning and no lumpy output. Maybe one of the genomes involved in the recombinant has a too small fraction represented and therefore would have not enough normal reads. That's why I was thinking to lower down the min value.

[ryanlayer]

Interesting! What happens when you run "samtools view $BAM | wc -l"?

On Thu, Dec 13, 2018 at 5:48 AM Fabou13 notifications@github.com wrote:

I am actually running lumpy on RNA viruses to detect recombinant genomes from two parental genomes. The output of SVtyper are fine for some samples and quite coherent. But I am having some samples for which I get the warning and no lumpy output. Maybe one of the genomes involved in the recombinant has a too small fraction represented and therefore would have not enough normal reads. That's why I was thinking to lower down the min value.

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[Fabou13]

Hi, I ran the command for two samples, here is what I got from the bam files: Sample 9: 7744319 Sample 10: 6580433 These two samples gave the Warning: only xx elements in distribution (min: 1000) Does it look abnormal to you? Thank you