Hiruna Samarakoon

In their [paper](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5445-3) it is mentioned as below, > **Paired-end version and 10X data** So far, only single-end read mapping is available for SQUAT. Namely, no paired-end information is required....

Thanks for the update @michxymi.

Hello @michxymi, Any updates on this? Thanks.

Hello @Theo-Nelson, This is happening because there are duplicate read ids in the blow5 file. Do you have a log how this file was created? ```` hiruna@hiruna-XPS-15-9500:~/Downloads$ slow5tools skim HCV_IVT_004_ALIGNED_SIGNALS.blow5...

Cool. I suppose this command will work ```` samtools view $BAM | cut -f 1 | sort -k1,1 | uniq | slow5tools get -o $BLOW5 ```` to check if the...

Hello @rugilemat Thanks for reporting this. Until we fix the conda issue can you download the executable to your HPC home directory as follows, ```` cd ${HOME} wget https://github.com/hasindu2008/slow5tools/releases/download/v1.1.0/slow5tools-v1.1.0-x86_64-linux-binaries.tar.gz tar...

Hey, I have some more examples that I think are related to this. The correct behavior should be POS+SVLEN==END, isn't it? It is not the case for 2,3,4,5 records. ````...

https://github.com/hasindu2008/slow5tools/commit/cd9ce920e70cf27df451f0db953bb9916b421a0c

Hi @mattloose, Thanks for getting back to me. It’s quite unlikely that any other process used the GPU during the readfish run — the system is dedicated solely to readfishing....