cerebis qc3C issues - Githubissues

cerebis / qc3C

Reference-free quality assessment for Hi-C sequencing data

GNU Affero General Public License v3.0

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Error: module 'numpy' has no attribute 'asscalar'

#63 shelkmike opened 1 year ago
2
Enzyme-free protocol

#62 gubrins closed 1 year ago
0
Support for Arima High coverage Hi-C kit

#61 Norbittner opened 2 years ago
7
Provide greater detail when BAM sort order is incorrect.

#60 cerebis closed 2 years ago
0
Failure to catch missing header exception

#59 cerebis closed 2 years ago
2
Parsing of BAM header when file is expected to be readname-sorted.

#58 agilly closed 2 years ago
7
Add ">20kbp" to the long-range pair counting statistic

#57 cerebis opened 3 years ago
0
Accommodating mismatches in ligation artefacts.

#56 cerebis opened 3 years ago
0
Input/Output documentation additiion

#55 cerebis closed 3 years ago
0
Increase the maximum separation computed for BAM mode.

#54 cerebis opened 3 years ago
0
Extended main help to better explain modes

#53 cerebis opened 3 years ago
0
Validate mapping minimum quality limit with other mapping tools.

#52 cerebis opened 3 years ago
0
Handling of split R1/R2 bam files

#51 cerebis opened 3 years ago
0
Duplicates, flags, tallying and MultiQC report

#50 cerebis opened 3 years ago
0
Add example data and results and extend docs

#49 cerebis opened 3 years ago
1
Rename jellyfish conda package

#48 cerebis opened 3 years ago
0
Old Linux distribution import error "GLIBC_2.23' not found"

#47 cerebis opened 3 years ago
4
Cut-site databases saved to filesystem are not backwards portable to older Python.

#46 cerebis opened 3 years ago
1
samtools missing from qc3C docker container path

#45 koadman closed 3 years ago
1
qc3c missing from path when run via singularity

#44 koadman closed 3 years ago
1
qc3C conda failure on CentOS8

#43 koadman opened 3 years ago
4
Validate performance when kmer mode is supplied unpaired read data.

#42 cerebis opened 3 years ago
0
Better bootstrap merged to master

#41 cerebis closed 3 years ago
0
Conda package import error and problems using Docker image

#40 cerebis opened 3 years ago
0
kmer lib creation options will not take effect of lib already exists

#39 cerebis closed 4 years ago
0
Mergine multidigest branch into master

#38 cerebis closed 4 years ago
0
Using longest ligation product can overestimate observed fraction

#37 cerebis opened 4 years ago
0
Check for input files as soon as possible

#36 cerebis opened 4 years ago
0
Natural occurrence estimation and correction

#35 cerebis closed 4 years ago
9
Add command line meta-options for well known commercial libraries

#34 cerebis closed 4 years ago
1
Environments with PYTHONPATH set can mislead docker image.

#33 cerebis opened 4 years ago
0
Handle restriction enzymes with ambiguous sites

#32 cerebis closed 4 years ago
1
Counting FastA returns 0

#31 cerebis closed 4 years ago
0
Add version and time stamps to JSON report

#30 cerebis closed 5 years ago
0
Add pigz to docker images

#29 cerebis closed 5 years ago
0
Denominator in long-range fraction

#28 cerebis closed 4 years ago
1
Kmer analysis is slow due to Jellyfish SWIG overhead.

#27 cerebis opened 5 years ago
0
Running singularity container without arguments produces esoteric error message

#26 cerebis closed 4 years ago
1
Improve docker useability after more use

#25 cerebis closed 4 years ago
1
qc3C depends on samtools

#24 cerebis closed 5 years ago
1
qc3C docker and singularity

#23 cerebis closed 5 years ago
1
Reports from kmer and bam modes should as consistent as possible.

#22 cerebis closed 5 years ago
0
Add docker/singlularity details to documentation

#21 cerebis closed 5 years ago
0
could track both full cut-site and vestigal

#20 cerebis closed 4 years ago
1
Validate on less commonly used enzymes

#19 cerebis closed 4 years ago
2
Fuzzier evidence of junctions

#18 cerebis closed 5 years ago
0
In bam mode, report fraction against long references

#17 cerebis closed 5 years ago
0
Output report in easily parsed format

#16 cerebis closed 5 years ago
1
Improve comment about fraction of reads starting with site

#15 cerebis closed 5 years ago
0
update read me for new CLI changes

#14 cerebis closed 5 years ago
0