Ali Barry

icon indicating a website link https://shorturl.at/pyB26

icon company University of Oxford icon location Bioinformatics and pain neurobiology. Joint University of Texas, Dallas and University of Vienna. Previously University of Oxford.

Results 3 comments of Ali Barry

Mapping error at .tmpMap//tmp.test2.*.SJ.out.tab'

Hiya, YAML is: ``` project: trial sequence_files: file1: name: /home/amb/patchseq/Undetermined_S0_R1_001.fastq.gz base_definition: - cDNA(23-50) - UMI(12-19) find_pattern: ATTGCGCAATG file2: name: /home/amb/patchseq/Undetermined_S0_R2_001.fastq.gz base_definition: - cDNA(1-50) file3: name: /home/amb/patchseq/Undetermined_S0_I1_001.fastq.gz base_definition: - BC(1-8) file4:...

Mapping error at .tmpMap//tmp.test2.*.SJ.out.tab'

Thanks for the quick reply. I removed all comments from the yaml, but am getting the same issues. Unmapped bam output is still generated, fails during the mapping stage. I...

Mapping error at .tmpMap//tmp.test2.*.SJ.out.tab'

Just updating for anyone else seeing the same issues - I never resolved this and instead switched to a kallisto-bustools pipeline, which now has a smart-seq3 option. See [biostars post](https://www.biostars.org/p/9552041/)....