hanyue36/nanoplexer

Tool for demultiplexing Nanopore barcode sequence data

nanoplexer's Issues

minimum alignment score options ignored

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

Please tag a release

https://github.com/hanyue36/demultiplexer/releases

needed for packaging

-h returns error code 1, should be 0

% demultiplexer -h
% echo $?
1
# should be 0

libgcc_s.so.1 must be installed for pthread_cancel to work

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.

memory overflow

your script request 170T memory , please fix it

Include barcode file assistance?

 -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?

Consider renaming the software

demultiplexer is a generic word.
have you considered renaming your software to something unique?

Have you driven single-cell RNA seq data sets?

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.

The format of barcode.fa

i am a new in nanopore data analysis, i am wondering the format of barcode.fa. Could u please show me a sample of barcode.fa？ or would it works if i just prepare the barcode.fa as the FASTA format, like that?