Comments (3)
I haven't done too much testing with the quality of inferring the fragment start position distribution with few samples. 5 million is probably overkill, as it's a fairly low-dimensional model --- you could try setting the number of burnin fragments to a lower number.
from salmon.
Is this the --numAuxModelSamples
parameter?
from salmon.
I would try and set both --numAuxModelSamples
and --numPreAuxModelSamples
to the same (lower) value --- maybe 100-200k.
from salmon.
Related Issues (20)
- (sorry for repeated reference from discussion)
- After using SAMtools to convert bam to fastq, the salmon quantification mapping rate is super low: is it normal?
- icu version conflict with libboost
- salmon quantmerge skipped the nucleotide IDs that have multiple sequences - Metagenome dataset HOT 2
- Precompiled asset missing for version 1.10.1
- Configure error installing salmon HOT 1
- rapidjson internal assertion failure: IsObject()
- Error running salmon
- Salmon installation problem HOT 3
- Difference between the genome browser view of BAM produced by STAR and the result of Salmon
- index error HOT 3
- Issues about using salmon quant on multiple bam files HOT 4
- transcript with very small EffectiveLength
- gene body coverage
- Segmentation core dumped - Salmon quant
- Counts in ONT data HOT 1
- Documentation - more explanation of percent_mapped and metadata information please HOT 1
- No bug - How to explain Salmon workflow simply ? (avoid mathematics-heavy explanation)
- Error (bug): version `GLIBC_PRIVATE' not found HOT 1
- Orphan recovery option in rare cases causes Salmon to quit abruptly without error
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from salmon.