Entering edit mode
Hello, Anyone,
I played with $ zUMIs-zUMIs.0.0.6/zUMIs-master.sh -f barcoderead_HEK.1mio.fq.gz -r cDNAread_HEK.1mio.fq.gz -n 1 -g /home/li/reference/hg38_chr22 -a /home/li/reference/hg38_chr22/GRCh38.84.chr22.gtf -c 1-6 -m 7-16 -l 50 -o /home/li/li01
.
In my output directory:
I only have *.aligned.sorted.bam.featureCounts
file but without *.ex.featureCounts
and *.in.featureCounts
.
If I put these two files in my directory, it runs well.
I tried to following https://github.com/sdparekh/zUMIs/issues/38, but no idea. Is that anything of the version Rsubread::featureCounts
?
Really appreciate any of your suggestion and help!
Best,
Yue
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.1