with *.aligned.sorted.bam.featureCounts but without *.ex.featureCounts or *.in.featureCounts

Question

[yueli7]

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. Is that any version wrong about Rsubread::featureCounts?

Really appreciate any suggestion and help!

Best,

yue

[ATpoint]

Github crossposted: https://github.com/sdparekh/zUMIs/issues/165

BioC crossposted: https://support.bioconductor.org/p/127921/

Same issue as: Error: All columns in a tibble must be 1d or 2d objects:

[ATpoint]

Is your ln command working normally as suggested in this GitHub issue? What is your operating system?

[yueli7]

Hello, ATpoint,

Thank you so much for your kindly response!

I am working on Ubuntu (Linux) system. I am trying to figure out this word.

"It seems that in your system, the "ln" command is missing. We use it to link the .ex and .in files!"

Thank you again for your great help！

Best,

Yue

$ sudo apt-get install ln
Reading package lists... Done
Building dependency tree       
Reading state information... Done
E: Unable to locate package ln

[ATpoint]

ln is a command for making symbolic links. What happens if you type ln?

[yueli7]

Hello, ATpoint,

Thank you so much for your great help!

$ ln
ln: missing file operand
Try 'ln --help' for more information.
$ ln --help
Usage: ln [OPTION]... [-T] TARGET LINK_NAME   (1st form)
or:  ln [OPTION]... TARGET                  (2nd form)
or:  ln [OPTION]... TARGET... DIRECTORY     (3rd form)
or:  ln [OPTION]... -t DIRECTORY TARGET...  (4th form)

Answer 1

[yueli7]

None files of 1.aligned.sorted.bam.ex.featureCounts and 1.aligned.sorted.bam.in.featureCounts .

If put the Examplezdata: test.aligned.sorted.bam.ex.featureCounts and test.aligned.sorted.bam.in.featureCounts in the oufolder li01, works well.

Till in zUMIs2.0, zUMIs-stats2.R has these two files.

zUMIs2.0 no problem.