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ngscat2's Introduction

Babelomics

Babelomics is an integrative platform for the analysis of Transcriptomics, Proteomics and Genomics data with advanced functional profiling

This version of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made using functional definitions, protein-protein interactions...

How to install

    git clone https://github.com/babelomics/babelomics.git
    cd babelomics/babelomics-web/
    bower install
    git submodule update --init
    cd lib/jsorolla/
    bower install

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ngscat2's Issues

program failed

--Hi,

runnning:
ngscat2 --bams ./SRR6823381.bam --bed ./Exome-Agilent.bed --out /work/ngscat --reference ./Homo_sapiens_hg38.fasta

it failed with:

Traceback (most recent call last):
File "ngscat2", line 8, in
sys.exit(main())
File "main.py", line 416, in main
generate_report(options, config)
File "/.local/lib/python3.7/site-packages/ngscat2/main.py", line 290, in generate_report
cover, _ = bam.myCoverageBed(options.bed, bedGraphFile=mainReporter.outdir)
File "/.local/lib/python3.7/site-packages/ngscat2/misc/bam_file.py", line 518, in myCoverageBed
endPositions.append(int(currentRead.aend))
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

how to identify the problem?
thank you --

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