QIAgen Targeted library #1730
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Hello, Thank you so much for mixer, it has proven to be a very valuable package for my Immune repertoire analysis. Very few reads aligned and it could be because the configuration of the library might be a little different. According to the vendor the library has phasing on both ends. Thank you so much for your help! 
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Replies: 3 comments 3 replies
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Hi, |
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thank you for your promt response! |
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Do you know the common sequence and the phasing size on each end? From the report I see that the pattern hasn't been identified meaning the primers were not found. |
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The information on the phased adapters the manufacturer provided is R1: start with TCR primer (7-10 nt from beginning). I1: 10nt index 1 I2: 10nt index 2 R2: start with UMI (with 14-18nt), it is before the common sequence ATG CAT TGG AGT CCT Could you please specify the settings recommended for this this library preparation for mouse? Thank you! |
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The command bellow should work. Did you manually check the common sequence is indeed present in the reads? |
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Hello
This has worked for me very well, thank you very much!
…________________________________
From: mizraelson ***@***.***>
Sent: Thursday, January 9, 2025 1:56 AM
To: milaboratory/mixcr ***@***.***>
Cc: Mateusz Pospiech ***@***.***>; Comment ***@***.***>
Subject: Re: [milaboratory/mixcr] QIAgen Targeted library (Discussion #1730)
The command bellow should work. Did you manually check the common sequence is indeed present in the reads? mixcr analyze qiagen-human-rna-tcr-umi-qiaseq \ --tag-pattern "^(R1: *)\^(UMI: N{14: 18})atgcattggagtcct(R2: *)" \ fastq. R1. fastq. gz \ fastq. R2. fastq. gz
The command bellow should work. Did you manually check the common sequence is indeed present in the reads?
mixcr analyze qiagen-human-rna-tcr-umi-qiaseq \
--tag-pattern "^(R1:*)\^(UMI:N{14:18})atgcattggagtcct(R2:*)" \
fastq.R1.fastq.gz \
fastq.R2.fastq.gz \
output
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Do you know the common sequence and the phasing size on each end? From the report I see that the pattern hasn't been identified meaning the primers were not found.
As a workaround you can try and add: