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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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mistake in isoseq refine documentation for single cell #637

Closed MengjunWu closed 7 months ago

MengjunWu commented 7 months ago

Hi,

I am following the single cell CLI Workflow for analyzing iso-seq data.

In Step 4 - Refine: the input files for isoseq refine are specified as:

.flt.bam or .flt.transcriptset.xml the actual command in the documentation is: isoseq refine .fl.5p--3p.bam primers.fasta .fltnc.bam --require-polya I understood ".fl.5p--3p.bam" should be the input for isoseq tag step while isoseq refine took output from isoseq tag? Just want to confirm if this is a mistake in the documentation and whether the correct input should be .flt.bam instead of .fl.5p--3p.bam? Many thanks, Mengjun
jmattick commented 7 months ago

Hi @MengjunWu, Thank you for opening this issue. You are correct. We run isoseq tag before isoseq refine. We will update the documentation to reflect this.

MengjunWu commented 7 months ago

Many thanks for the reply.

There is another problem with isoseq tag, When I run the command, it does not return the flt.transcriptset.xml file. I think it suppose to generate both bam and xml file?