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I have a problem with very low alignment rate 137/1.6million reads using Qiaseq TCR mouse preset.
I have checked few unaligned reads with BLAST and all mapped to TCR regions.
I have also tried to swap read1 and read2 but the alignment rate goes to 0.
Some online discussion suggest trimming the qiaseq primer/adapter then use general-amplicon-with-umi preset.
But I couldn't find the primer/adapter sequences online and my MiXCR v4.6 can't validate that general amplicon presets (command: miscr listPresets)
Any help would be very appreciated.
Thank you,
Rad
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Hi,
I have a problem with very low alignment rate 137/1.6million reads using Qiaseq TCR mouse preset.
I have checked few unaligned reads with BLAST and all mapped to TCR regions.
I have also tried to swap read1 and read2 but the alignment rate goes to 0.
Some online discussion suggest trimming the qiaseq primer/adapter then use general-amplicon-with-umi preset.
But I couldn't find the primer/adapter sequences online and my MiXCR v4.6 can't validate that general amplicon presets (command: miscr listPresets)
Any help would be very appreciated.
Thank you,
Rad
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