Correct_UMI
Description
Correct UMIs with Set Cover algorithm.
Corrects all UMIs in the given bam file.
Algorithm originally developed by Victoric Popic.
Data Requirements:
- Bam file should be aligned and annotated with genes and transcript equivalence classes prior to running.
- It is critical that you give the proper input for the
--pre-extractedflag.- If the file has been run through
longbow extract, use--pre-extracted - If the file has NOT been run through
longbow extractDO NOT USE--pre-extracted
- If the file has been run through
The following tags are required in the input file:
CBJX(Adjusted UMI - Configurable)eq(Equivalence class assignment - Configurable)XG(Gene assignment - Configurable)rq(Read Quality: [-1.0, 1.0])JB(Back / UMI trailing segment Smith-Waterman alignment score - Configurable)
Command help
$ longbow correct_umi --help
Usage: longbow correct_umi [OPTIONS] INPUT_BAM
Correct UMIs with Set Cover algorithm.
Options:
-v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or
DEBUG
--cache-read-loci Dump and read from a cache for the read
loci, if possible.
--max-ccs-edit-dist INTEGER Maximum edit distance between a CCS read and
a target to consider them both part of a
group of UMIs [default: 2]
--max-clr-edit-dist INTEGER Maximum edit distance between a CLR read and
a target to consider them both part of a
group of UMIs [default: 3]
--max-ccs-length-diff INTEGER Maximum length difference between a CCS read
and a target to consider them both part of a
group of UMIs [default: 50]
--max-clr-length-diff INTEGER Maximum length difference between a CLR read
and a target to consider them both part of a
group of UMIs [default: 150]
--max-ccs-gc-diff FLOAT Maximum GC content difference between a CCS
read and a target to consider them both part
of a group of UMIs [default: 0.05]
--max-clr-gc-diff FLOAT Maximum GC content difference between a CLR
read and a target to consider them both part
of a group of UMIs [default: 0.15]
--max-ccs-umi-length-delta INTEGER
Maximum length difference between the UMI of
a CCS read and the given UMI length to be
included in the loci for possible
correction. [default: 3]
--max-clr-umi-length-delta INTEGER
Maximum length difference between the UMI of
a CLR read and the given UMI length to be
included in the loci for possible
correction. [default: 4]
--max-final-ccs-umi-length-delta INTEGER
Maximum length difference between the final,
corrected UMI of a CCS read and the given
UMI length to be included in the final good
results file. [default: 3]
--max-final-clr-umi-length-delta INTEGER
Maximum length difference between the final,
corrected UMI of a CLR read and the given
UMI length to be included in the final good
results file. [default: 3]
--min-back-seg-score INTEGER Minimum score of the back alignment tag for
a read to be included in the final good
results file. [default: 10]
--umi-tag TEXT Tag from which to read in UMIs from the
input bam file. [default: JX]
--gene-tag TEXT Tag from which to read in gene IDs from the
input bam file. [default: XG]
--eq-class-tag TEXT Tag from which to read in read transcript
equivalence classes (i.e. transcript IDs)
from the input bam file. [default: eq]
--final-umi-tag TEXT Tag into which to put final, corrected UMI
values. [default: BX]
--umi-corrected-tag TEXT Tag into which to put whether a given UMI
was actually corrected. [default: UX]
--back-alignment-score-tag TEXT
Tag containing the back (trailing adapter)
alignment score. [default: JB]
-l, --umi-length INTEGER Length of the UMI for this sample.
[default: 10]
-o, --output-bam PATH Corrected UMI bam output [default: stdout].
-x, --reject-bam PATH Filtered bam output (failing reads only).
-f, --force Force overwrite of the output files if they
exist.
--pre-extracted Whether the input file has been processed
with `longbow extract`
--help Show this message and exit.
Examples
$ longbow correct_umi -f --cache-read-loci --pre-extracted -l 10 -o tmp.umi_corrected.bam -x tmp.umi_rejected.bam tmp.bam
[INFO 2022-11-07 13:44:53 correct_umi] Invoked via: longbow correct_umi -f --cache-read-loci --pre-extracted -l 10 -o tmp.umi_corrected.bam -x tmp.umi_rejected.bam tmp.bam
[E::idx_find_and_load] Could not retrieve index file for 'tmp.bam'
[INFO 2022-11-07 13:44:53 correct_umi] Writing UMI corrected reads to: tmp.umi_corrected.bam
[INFO 2022-11-07 13:44:53 correct_umi] Writing reads with uncorrectable UMIs to: tmp.umi_rejected.bam
[INFO 2022-11-07 13:44:53 correct_umi] Creating locus -> read map...
Extracting Read Groups: 108 read [00:00, 25018.49 read/s]
[INFO 2022-11-07 13:44:53 correct_umi] Number of reads: 0
[INFO 2022-11-07 13:44:53 correct_umi] Number of valid reads: 95
[INFO 2022-11-07 13:44:53 correct_umi] Number of filtered by gene: 1
[INFO 2022-11-07 13:44:53 correct_umi] Number of filtered by UMI: 12
[INFO 2022-11-07 13:44:53 correct_umi] Writing locus2reads cache: tmp.bam.locus2reads.pickle
[INFO 2022-11-07 13:44:53 correct_umi] done. (elapsed: 0.001016855239868164s)
[INFO 2022-11-07 13:44:53 correct_umi] Number of loci: 19
[INFO 2022-11-07 13:44:53 correct_umi] Correcting reads at each locus...
[INFO 2022-11-07 13:44:53 correct_umi] Done. Elapsed time: 0.02s. Overall processing rate: 6224.46 reads/s.
[INFO 2022-11-07 13:44:53 correct_umi] Number of reads with corrected UMIs: 86/108 (79.63%)
[INFO 2022-11-07 13:44:53 correct_umi] Number of reads with uncorrectable UMIs: 22/108 (20.37%)
[INFO 2022-11-07 13:44:53 correct_umi] Total Number of reads: 108