Question: are the intermediate BAM files saved?

SpatialTranscriptomicsResearch / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

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Question: are the intermediate BAM files saved? #112

Closed Puriney closed 4 years ago

Puriney commented 4 years ago

Hello ST team, I was wondering if the intermediate BAM files are saved somewhere? Best, Yun

JSheng2023 commented 4 years ago

I think the ST pipeline generates a bed file in the output folder and you can try to convert it to sam file using bedToSam function included in BEDtools.

Puriney commented 4 years ago

--temp-folder $TEMPDIR \
--no-clean-up

By calling the arguments above, the pipeline saves the intermediate results including the BAM file I am asking here. It is saved '$TEMPDIR/annotated.bam'. Thank you for following up.