Comments (4)
The command you use assumes that the barcode is at a fixed position in the read, the location of which can be specified using the -s
and -e
options.
I assume though, that your barcodes are not at a fixed position, for these cases the match
command can be used. This command indeed also checks the reverse complement.
from demultiplex.
It works! Thank you for the swift reply!
By the way, are the barcodes also trimmed from the demultiplexed sequences? At a first sight it appears not.
from demultiplex.
No, the reads remain unchanged.
from demultiplex.
Thanks! Have a nice day.
from demultiplex.
Related Issues (20)
- demultiplex match outputs all input reads to each barcode HOT 3
- dealing with conflicts HOT 5
- Output HOT 12
- tags 5' and 3' in two different files usage HOT 1
- Paired end support for match. HOT 2
- Dual barcodes with match HOT 3
- demultiplexing illumina with forward and reverse tag HOT 1
- positions for barcodes do not work at all! HOT 1
- Degenerated constructs HOT 5
- Does demultiplex support hamming distance? HOT 1
- All reads go into unknown HOT 4
- Is it possible for the barcode to contain non-ATCG characters? HOT 1
- demultiplex unknown results HOT 4
- pairwise2.py doesn't work. Biopython deprecated it. HOT 4
- Does demultiplex pick up where it left off? HOT 1
- Does this tool works for Cell hashing data generated for cell ranger multi? HOT 3
- Demultiplex cannot separate read-pairs by R1 barcode and R2 barcode simultaneously if at least either of the two is found HOT 10
- Demultiplex v1.2.2 misses barcodes starting with a (series of) DELetions aka supposedly incompletely amplified PCR products HOT 11
- Demultiplex with i7 index on dual index FASTQ HOT 2
- demultiplex does not find any barcodes if -e NUM is larger than lenghth of the shortest actually provided barcode in a TSV file HOT 11
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