Comments (1)
I ended up re-running the whole thing with the chosen feature model, but it seems like the BAM files are very similar (perhaps up to some multi-mapping?). In the CellReads.stats
files, the number of CB matches and total UMIs are the same, and the genomeU
and genomeM
columns are the same in the outputs.
So my impression is that like it might be possible to rerun the quantification from an existing BAM file, and this would be quite handy for trying out different models (and also for things like subsampling analysis). Does that seem like a reasonable thing to add?
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Related Issues (20)
- STAR alignments generate different counts: Full genome vs Split genome
- fatal error, cannot create output file for unmapped.out.mate1.thread0
- Possible to implement special treatment of multi-gene reads for BCR/TCR genes?
- [Version 2.7.11b] - Error running 'make' command HOT 6
- killed after "...starting to generate Genome files"
- Problem with reading FASTQ files
- secondary alignment bit in flag not set for unmapped mate of a pair with the other mate mapped
- Parameters for 10x 5' alignment HOT 1
- Chimeric reads very high
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- --quantMode GeneCounts output lacks two T-cell receptor genes compared to htseq-count
- STAR hangs at 300% CPU
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- Alignement of viral genome with reads from infected host
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- STARSolo, alignment of Scell from different lanes
- FATAL ERROR in input read file: the total length of barcode sequence is 151 not equal to expected 28, and also not mapped reads HOT 1
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