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License: MIT License
Tool for demultiplexing Nanopore barcode sequence data
License: MIT License
It seems that the "-s" option for the alignment score is unused or I may be entering it incorrectly. I have tried multiple rounds with varying "s" scores above the default of "22", and the alignment score values are not changed in the log or in the amount of demultiplexed samples.
Command:
$ ./nanoplexer/nanoplexer -b ./barcodes.fa -d sample.txt -s 40 -p ./output -l log ../FAO23974_pass_ced4ad01_125.fastq
stdout:
2022-02-07 13:57:02 Minimal alignment score is 22
2022-02-07 13:57:04 Finished demultiplexing sequence data.
$ head log:
0f900e08-52dd-4cb7-a5df-4ec45b9464ef REVERSE10 + 42 H_REV + 42
1e1e0c4c-21cf-41d6-af1c-d63bd591d8ea REVERSE01 + 33 A_REV + 29
19be82b8-1094-4b90-8cf5-1db5d045f484 REVERSE02 + 42 E_REV + 42
c8a67fd7-29d2-4374-b4ab-3243d4647ffe REVERSE03 + 31 A_REV + 42
4de7e4c5-e8e2-4ee0-8a0c-708ad3a7a31b REVERSE01 + 42 F_REV + 42
069fd321-f80c-4cb1-91c1-1e7196597bcf H + 42 REVERSE08_REV + 32
e6df5bca-c01f-402f-9f6c-f3837786a1b0 E + 42 REVERSE03_REV + 34
aa3a79b1-1691-4350-bc51-362188635966 REVERSE02 + 32 E_REV + 42
20161ea4-e32a-4da1-bafa-63e4602202fe REVERSE01 + 28 D_REV + 38
c461726f-5090-4c11-94f8-3ce608865f4d REVERSE01 + 42 F_REV + 42
After install nanoplexer with command conda install -c bioconda nanoplexer
, I try to use nanoplexer -b barcode.fa -p oput_dir -t 20 input.clean.fastq
to demultiplex,but I got Error:
2021-03-25 04:12:50 Minimal alignment score is 17
libgcc_s.so.1 must be installed for pthread_cancel to work
libgcc_s.so.1 must be installed for pthread_cancel to work
libgcc_s.so.1 must be installed for pthread_cancel to work
Aborted (core dumped)
The I try to install verson 0.1.2, 0.1.1 and 0.1 in conda, error still rasise.
Then I try to clone repository and make
, but still got error:
option.c: In function 'opt_set_mat':
option.c:25:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for (j = 0; j < 4; ++j)
^~~
option.c:27:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
mat[k++] = 0;
^~~
Though still can got an executable file,but got error same as conda version.
Can you help me? Thank you so much.
your script request 170T memory , please fix it
https://github.com/hanyue36/demultiplexer/releases
needed for packaging
-d FILE dual barcode pair file
maybe convert these
https://github.com/nanoporetech/qcat/tree/master/qcat/resources/kits
and include them in the github?
can you auto-detect?
Hi,
Could you please tell me a bit more about the batch option?
All my reads are merged into a huge file (the result after a combined simplex + duplex basecalling) and nanoplexer crashes with a segmentation fault when I launch it. However, if I try on a subset of the file with 4000 reads, the program does work, so I'm wondering if I need to increase this batch size option or split my merged reads, or something else.
Thanks,
Ana
% demultiplexer -h
% echo $?
1
# should be 0
I was wondering if nanoplexer could deal with barcodes known from MiSeq run on a 10x run sequenced on MinION?
The no. of barcodes is around 1200. I tried with poreplex and it just shutdown as it opened to many concurrent fastq files.
Hi,
When I try to use fastqs from dorado --emit_fastq, nanoplexer spits out the wrong format for demultiplexed fastqs where it is missing the name row.
Do you know what the cause of that is? It works fine with guppy outputted fastq files.
Thanks,
Jacky
demultiplexer
is a generic word.
have you considered renaming your software to something unique?
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