laozzzzz / bartender-1.1 Goto Github PK

i'm interested in using this software in my project but hesitating because there is no license.

Hi, I just tried to install and run bartender, but following the example provided in the README file, I ran into a "regex_error" in the extraction step:

$ bartender_extractor_com -f 2M_test.fq -o 2M_extracted -q ? -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA -m 2
Running bartender extractor
bartender_extractor 2M_test.fq 2M_extracted 63 "(TAC.|TA.C|T.CC|.ACC)([ATCGN]{4,7})(AA)([ATCGN]{4,7})(AA)([ATCGN]{4,7})(TT)([ATCGN]{4,7})(ATA.|AT.A|A.AA|.TAA)" TACC ATAA 9 1
terminate called after throwing an instance of 'std::regex_error'
what(): regex_error

OS version is CentOS 7 (Core)
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

Please help me resolve this problem. Thanks for your help!

Hi,

I was asked to extract UMIs from given reads. Our sequences should be in the following format where 5' and 3' sequences are shown. T in umi sequence is constant.

AGATTGATCTAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNTNNNNTCCATGAGACTCCTGAGTCAGAGGCAAAGGCTTTTACTGCTCACAGCTTAGCAGACAGCATGAGGTTCATGTTCACAT

I ran extractor like below.

bartender_extractor_com -f ../UMI_r2.fastq -p GATCT[5]T[4]TCCAT -o r2_results_1.1 -d both

However in the resulting barcode file all of the sequences are always 9 bp. where shouldnt it be 10? since my umi sequence is NNNNNTNNNN

Because of the 9 bps problem, i couldn't run the umi mode as well.

A little guidance would totally be appreciated.

Best regards,

Tunc.

Extractor and Combiner both build correctly, but make bartender_single fails on Ubuntu 21.10. make bartender_single gives the following error that I've attached as an image:

Adding #include <cstdint> to mixturebptester.cpp and mixturebptester.h gets rid of that part of the error, but the other errors like size_t being undeclared, etc. are still there.

Dear Lao,

Thank you for your package. Can someone extract the sequencing depth over time through bartender?
Looking forward to your answer

with best wishes,

Our IT has had issues installing:
" consistently get the same error despite using various combinations of OS, gcc and boost versions to compile this software:
bartender_single: src/bartender_single.cpp:174: int main(int, char**): Assertion `argc >= 3' failed."

Hi, I just tried to install and run bartender, but following the example provided in the README file, i ran into a "regex_error" in the extraction step:

$ bartender_extractor_com -f 2M_test.fq -o 2M_extracted -q ? -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA -m 2
Running bartender extractor
bartender_extractor 2M_test.fq 2M_extracted 63 "(TAC.|TA.C|T.CC|.ACC)([ATCGN]{4,7})(AA)([ATCGN]{4,7})(AA)([ATCGN]{4,7})(TT)([ATCGN]{4,7})(ATA.|AT.A|A.AA|.TAA)" TACC ATAA 9 1  
terminate called after throwing an instance of 'std::regex_error'
  what():  regex_error

OS version is CentOS 7 (Core), kernel 3.10.0-1062.9.1.el7.x86_64

GCC version is 4.8.5 20150623 (Red Hat 4.8.5-39)

Thanks for your help!

Do you mean a incorrect merge destroy such function?

Which tools can I use to do this.

I don't know if anyone is still maintaining this repo, but I was looking at the details of some clustering results with a new dataset, and I noticed that the clustering algorithm is merging sequences with a Hamming distance greater than the -d parameter.

With the -d parameter set to 3, I found one cluster that contains sequences with Hamming distance up to 6 from the cluster center.
The command line call I'm using is:

python ~/bartender-1.1/bartender_single_com -f 2023-09-26_test_12_lintags.txt -o 2023-09-26_test -c 100 -z 5 -l 5 -s 1 -t 4 -d 3

I have a relatively small barcode data file that reproduces the problem, but it is still too big to attach here (200 MB). So, if anyone is interested, let me know, and I'll send it to you for verification and testing.

Thanks-

Hi,

When I try to run bartender_extractor_com I get the following error:
"-bash: bartender-1.1-master/bartender_extractor_com: /usr/bin/python: bad interpreter: No such file or directory"

I checked my python installation and deactivated the conda environment.
I have "/usr/bin/python3" directory, but not "/usr/bin/python."

I also tried to alias python with python3 and the problem still persists.

Here is my system information:
macOS Monterey 12.5

Apple clang version 13.0.0 (clang-1300.0.29.30)
Target: x86_64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Python 3.10.7

I would be glad if you could help me with this issue. Thank you.