I have just started using Alevin and I have few basic queries. And I am asking this because I couldn’t find it in the documentation
-
How to know how many reads are uniquely mapping and how many are multi mapping when doing quantification with Alevin.
-
The
alevin_meta_info.json
saysNumber of mapped reads
. Are these Uniquely+multimappig reads or just Uniquely mapping reads. - For all of my samples the library type couldn’t be determined. I got the following log for example. I used
ISR
since the data was generated from Chromium 3′ V3 chemistry.
"expected_format": "ISR",
"compatible_fragment_ratio": 1.0,
"num_compatible_fragments": 11147644,
"num_assigned_fragments": 11147644,
"num_frags_with_concordant_consistent_mappings": 0,
"num_frags_with_inconsistent_or_orphan_mappings": 15681780,
"strand_mapping_bias": 0.0,
"MSF": 0,
"OSF": 0,
"ISF": 0,
"MSR": 0,
"OSR": 0,
"ISR": 0,
"SF": 0,
"SR": 0,
"MU": 0,
"OU": 0,
"IU": 0,
"U": 0
- When I run AlevinQC why the
Number of used reads
(which Alevin documentation says are reads that are used for quantification)greater
thanNumber of mapped reads
.
I am using the following command
~/salmon-1.5.2_linux_x86_64/bin/salmon alevin -l ISR -1 R1_001.fastq.gz -2 R2_001.fastq.gz --chromiumV3 --dumpFeatures --dumpMtx --expectCells 200 -i salmon_index/ -p 20 -o sample1 --keepCBFraction 1 --numCellBootstraps 100 --tgMap tx2gene.txt &
- When I set
--keepCBFraction 1
, does setting--expectCells 200
make sense. I am asking this because I didn’t see any change in mapping percentages of reads and cell barcodes being thrown out when I use both.
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