Mercurial > repos > iuc > schicexplorer_schicmergematrixbins

annotate test-data/scHicQualityControl/qc_report_chr1_chr2.txt @ 2:47ef02546fe9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:24:20 +0000
parents 18ac7f83ae0e
children
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18ac7f83ae0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
1 # QC report for single-cell Hi-C data generated by scHiCExplorer 1-dev
18ac7f83ae0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
2 scHi-C sample contained 20 cells:
18ac7f83ae0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
3 Number of removed matrices containing bad chromosomes 0
18ac7f83ae0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
4 Number of removed matrices due to low read coverage (< 100000): 8
18ac7f83ae0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
5 Number of removed matrices due to too many zero bins (< 0.001 density, within 30000000 relative genomic distance): 0
18ac7f83ae0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff changeset
6 12 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore.