Mercurial > repos > iuc > schicexplorer_schicadjustmatrix

annotate test-data/scHicQualityControl/qc_report.txt @ 1:799a9fe1265c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:13:23 -0400
parents fad89d56674a
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799a9fe1265c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
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1 # QC report for single-cell Hi-C data generated by scHiCExplorer 4
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fad89d56674a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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diff changeset
2 scHi-C sample contained 20 cells:
fad89d56674a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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3 Number of removed matrices containing bad chromosomes 0
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799a9fe1265c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
4 Number of removed matrices due to low read coverage (< 100000): 10
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fad89d56674a "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
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799a9fe1265c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
6 10 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore.