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error when uploading clonotype file from mixcr4.2.0

Open github-wow opened this issue 2 years ago • 0 comments

Hi,

mixcr3.0.13 generates clonotype txt files with the following columns (cloneCount, cloneFraction, etc.):

cloneId	cloneCount	cloneFraction	targetSequences	targetQualities	allVHitsWithScore	allDHitsWithScore	allJHitsWithScore	allCHitsWithScore	allVAlignments	allDAlignments	allJAlignments	allCAlignments	nSeqFR1	minQualFR1	nSeqCDR1	minQualCDR1	nSeqFR2	minQualFR2	nSeqCDR2	minQualCDR2	nSeqFR3	minQualFR3	nSeqCDR3	minQualCDR3	nSeqFR4	minQualFR4	aaSeqFR1	aaSeqCDR1	aaSeqFR2	aaSeqCDR2	aaSeqFR3	aaSeqCDR3	aaSeqFR4	refPoints
0	1091	0.0050558882	TGTGCTTGTCAAGCTCATTTACTCACGGGAGGAGGAAACAAACTCACCTTT	[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[	TRAV38-2DV8*00(811.6)		TRAJ10*00(314.4)	TRAC*00(89.6)	433|440|469|0|7||35.0		21|53|84|19|51||160.0												TGTGCTTGTCAAGCTCATTTACTCACGGGAGGAGGAAACAAACTCACCTTT	58								CACQAHLLTGGGNKLTF		:::::::::0:-9:7:::::19:-1:51:::

mixcr4.2.0 generates clonotype tsv files with the following columns (readCount, readFraction, etc.):

cloneId	readCount	readFraction	uniqueMoleculeCount	uniqueMoleculeFraction	targetSequences	targetQualities	allVHitsWithScore	allDHitsWithScore	allJHitsWithScore	allCHitsWithScore	allVAlignments	allDAlignments	allJAlignments	allCAlignments	nSeqCDR3	minQualCDR3	aaSeqCDR3	refPoints
0	14506	0.0025839094	283	0.0025100446	TGTGCTCTGAGTGAGGTAAACGACTACAAGCTCAGCTTT	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	TRAV19*00(825.4)		TRAJ20*00(259.3)	TRAC*00(89.7)	432|448|469|0|16||80.0		25|46|77|18|39||105.0		TGTGCTCTGAGTGAGGTAAACGACTACAAGCTCAGCTTT	45	CALSEVNDYKLSF	:::::::::0:-1:16:::::18:-5:39:::

it seems it does not allow to upload mixcr4 clonotype files in VDJViz

github-wow avatar Feb 07 '23 12:02 github-wow