Positive splicing events are not be detected #228
Comments
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I believe there has been other reports that some of the parameters in
leafcutter do not work as intended, including when reducing the minimum
number of reads too much. We are working on re-writing leafcutter with
python3 and add functionality plus bug fixes, but we only expect to release
it late this year.
…On Thu, Feb 23, 2023, 21:50 ym-chen ***@***.***> wrote:
Hi,
I use the Leafcutter to analyze a batch of samples. One of the samples has
a splice event in the region: chr7:116411552-116415165, and the other
samples are negative. But I can't find any splicing event in the positive
region from the result file of leafcutter. I wonder how leafcutter process
this data. The specific parameters of leafcutter which I run the data like
the following:
leafcutter_cluster.py -m 2 -M 1 -l 500000
leafcutter_ds.R --min_samples_per_intron=1 --min_samples_per_group=0 --timeout=300 --min_coverage=0
The first data, I can find the junction site in the positive.junc. And
also can find the intron-cluster in perind_numers.counts.gz. The number 0
in perind_numers.counts.gz is the junction count of negative samples (total
11 negative samples). But in the DAS_cluster_significance.txt, I find the
cluster is filtered. It seems like some parameter(s) works. And how can I
change my parameters?
## positive.junc
chr7 116411708 116414934 . 7 -
chr7 116411708 116411902 . 4 -
chr7 116411708 116414934 . 2 +
## perind_numers.counts.gz
chr7:116411708:116411903:clu_63826_NA 0 0 0 0 0 4 0 0 0 0 0 0
chr7:116411708:116414935:clu_63826_NA 0 0 0 0 0 9 0 0 0 0 0 0
## DAS_cluster_significance.txt
chr7:clu_63826_NA <=1 sample with coverage>0 NA NA NA NA MET
The second data, I can find the junction site in the positive.junc, but
can't find the intron-cluster in positive.junc.Batch.sorted.gz and
perind_numers.counts.gz. I set the --minreads=1, but why is it still not
clustered?
## positive.junc
chr7 116412043 116414934 . 1 +
chr7 116411708 116414934 . 11 -
chr7 116411708 116414934 . 11 +
This is very important to me, hope to get your help.
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I checked the log file, but still can't find the exact reason. I may do more test in the future. Thanks for your reply.
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Hi,
I use the Leafcutter to analyze a batch of samples. One of the samples has a splice event in the region: chr7:116411552-116415165, and the other samples are negative. But I can't find any splicing event in the positive region from the result file of leafcutter. I wonder how leafcutter process this data. The specific parameters of leafcutter which I run the data like the following:
The first data, I can find the junction site in the positive.junc. And also can find the intron-cluster in perind_numers.counts.gz. The number 0 in perind_numers.counts.gz is the junction count of negative samples (total 11 negative samples). But in the DAS_cluster_significance.txt, I find the cluster is filtered. It seems like some parameter(s) works. And how can I change my parameters?
The second data, I can find the junction site in the positive.junc, but can't find the intron-cluster in positive.junc.Batch.sorted.gz and perind_numers.counts.gz. I set the --minreads=1, but why is it still not clustered?
This is very important to me, hope to get your help.
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