How to set the correct preset for my data #1870
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pandahui01
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Hi, yes the 10x-bulk.yaml preset should work, but you will have to specify the pattern manually that describes you UMI structure. |
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This is my align.txt
Analysis time: 31.56s
Total sequencing reads: 9035215
Successfully aligned reads: 529014 (5.86%)
Coverage (percent of successfully aligned):
CDR3: 431900 (81.64%)
FR3_TO_FR4: 405582 (76.67%)
CDR2_TO_FR4: 404692 (76.5%)
FR2_TO_FR4: 394254 (74.53%)
CDR1_TO_FR4: 393549 (74.39%)
VDJRegion: 412315 (77.94%)
Alignment failed: no hits (not TCR/IG?): 6828336 (75.57%)
Alignment failed: absence of V hits: 5955 (0.07%)
Alignment failed: absence of J hits: 1671910 (18.5%)
I looked at the previous preset discussion and used 10x-bulk.yaml because my data came with umi, and did breaks to allow it to be assembled into a full-length sequence (PE150)
Can you help me? Thank you!
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