Comments (2)
I meet the same problem.
Anyone can help?
from eclipdemux.
Hi both,
I run the script without installing it:
(base) niek@desktop:.../scripts$ git clone [email protected]:niekwit/eclipdemux.git
(base) niek@desktop:.../scripts$ python eclipdemux/eclipdemux_package/demux.py --help
Usage: takes raw fastq files and demultiplex inline randomer and adapter sequences
Options:
-h, --help show this help message and exit
--dataset=DATASET
--newname=NEWNAME
-m METRICSFILE, --metrics=METRICSFILE
--fastq_1=FASTQ1 fastq file to barcode demux
--fastq_2=FASTQ2 fastq file to barcode demux
--expectedbarcodeida=EXPECTEDBARCODEIDA
--expectedbarcodeidb=EXPECTEDBARCODEIDB
-b BARCODESFILE, --barcodesfile=BARCODESFILE
reference barcodes fasta or tsv file (tsv columns:
barcode_sequence/barcode_id)
--length=RANDOMER_LENGTH
Length of randomer sequence at front of 2nd read
--max_hamming_distance=ALLOWED_DISTANCE
Max Hamming distance between read barcode and given
barcodes to assign a barcode to a read
--legacy
After you have fixed the izip
import error (see my fork), you can run the script (Python 3.10.10)
from eclipdemux.
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from eclipdemux.