Comments (4)
jfjlaros
commented on August 25, 2024
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.
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ViriatoII
commented on August 25, 2024
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.
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jfjlaros
commented on August 25, 2024
No, the reads remain unchanged.
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ViriatoII
commented on August 25, 2024
Thanks! Have a nice day.
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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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