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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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creating SJ.out.tab in zUMIs #292

Closed kwglam closed 2 years ago

kwglam commented 2 years ago

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

cziegenhain commented 2 years ago

Hi,

In the current implementation for zUMIs, there are 2 scenarios with regards to STAR:

  1. If starting from the Filtering stage (ie beginning of the pipeline) and a sufficiently high memory limit (>= 2x the reference genome size), zUMIs will run several jobs of STAR in parallel and concatenate the output bam files. You will not get the SJ out file from the individual jobs.
  2. If starting the pipeline from "which_stage: Mapping" or when a small memory limit is set, a single STAR job is run and you should just find the SJ.out.tab in your zUMIs run folder.

Best, Christoph

kwglam commented 2 years ago

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

cziegenhain commented 2 years ago

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.

kwglam commented 2 years ago

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!

cziegenhain commented 2 years ago

I don't think that's going to be possible.