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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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/count folder empty #157

Closed Magisterh1 closed 5 months ago

Magisterh1 commented 5 months ago

Hi!

I tried to run the docker version of slamdunk all, and received the expected files in the folders /filter /map and /snp. The /count folder is generated, but it does not contain any file.

Could you suggest, how to proceed?

Many thanks!!

Magisterh1 commented 5 months ago

ok, I guess I solved the problem. I initially processed the fastq files using trim_galore and I did not specify the -rl 100 in slamdunk all. I retried with -rl 100 and received the count files, however, all counts were zero. Thus, I re-ran the pipeline using raw fastq files as input. Now everything looks as expected.