Closed kwglam closed 2 years ago
Hi,
In the current implementation for zUMIs, there are 2 scenarios with regards to STAR:
Best, Christoph
Hi Christoph,
Thanks for replying! I ran the pipeline again with "which_stage: Mapping", it gave me this error:
EXITING because of FATAL INPUT ERROR: --readFilesType SAM requires specifying SE or PE reads SOLUTION: specify --readFilesType SAM SE for single-end reads or --readFilesType SAM PE for paired-end reads
And then I tried to follow the suggestion by adding "--readFilesType BAM PE" or "--readFilesCommand samtools view" in the additional STAR parameter (my input is BAM file), it gave another error:
EXITING: FATAL INPUT ERROR: duplicate parameter "readFilesType" in input "Command-Line" SOLUTION: keep only one definition of input parameters in each input source
Any insights??
Thanks, Gabriel
There should be a .run.yaml that zUMIs adds some information to during the pipeline execution, sorry I forgot to mention that it would have been better to use that one. zUMIs always keeps the original yaml untouched and writes a copy which is named .run.yaml
You can add a line with read_layout: SE
(or PE) depending on if you have single or paired cDNA reads.
Thanks! It works great with the 'read_layout: SE' line.
I am working on some Smart-seq3 data and wondering if zUMIs can generate SJ.out.tab for individual cells instead? Thanks!
I don't think that's going to be possible.
Hi,
I would like to create a SJ.out.tab file generated from STAR in zUMIs. Do you know how to do it? Thanks!
Gabriel