Open wong-ziyi opened 2 years ago
@wong-ziyi Thanks for the issue!
I think I might understand the error.
The warning NAs introduced by coercion to integer range
sometimes means that some number reached the maximum number size (2,147,483,648).
I will try to debug the code, but other issues may also be triggered later on. The easiest for me would be for you to share the bam files. Would that be possible?
@mzytnicki Thanks so much for your quick reply.
I attached two bam files below.
https://www.dropbox.com/sh/pc9ceapgg0kr9gc/AADgsHYnUZciiiNkqbTe55rKa?dl=0
Hope two bam files are enough for you because my dropbox space was already full.
P.S. the index file was generated using samtools index -b
.
@wong-ziyi Thanks! I will to debug it ASAP. I will keep you updated.
@mzytnicki I now just finished reading the article related to this software. I am sorry that I misunderstood the purpose of srnadiff. I was planned to use srnadiff for alternative splicing analysis. In my original thinking, srnadiff can output the differential expressed region, and then I can classify those regions into different types of alternative splicing according to their genome coordinate and the genome annotation. I think this error is due to my larger mRNA sequencing files than normal sRNA sequencing results, maybe?
Do you think the above workflow is suitable? If not, I am so sorry to bother you.
@wong-ziyi Well, I did not try. However, I do not expect it to work, since the package was created with small RNA analysis in mind. I have never tried, but I would be glad if that worked!
That said, another package derfinder, was made for messenger RNA analysis. I do not know, however, if it works for alternative splicing...
@wong-ziyi Anyway, if you want to give srnadiff a try, you can.
library(devtools)
install_github("mzytnicki/srnadiff")
Does that work?
Hi,
When I run the srnadiffExp() I got warning message as below:
And the srnaExp object looks like this:
Since there are all NaN in normaFactors of srnaExp, srnadiff(srnaExp,nThreads=64) can not run appropriately:
Below is the session info:
The .bam files were generated using STAR software with the parameters below:
sample information:
paths to the BAM files:
annotation:
Should I filter out some reads in my bam files to avoid such errors? If so, what reads should I remove? Or, should I change something when running the STAR software?