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Old 01-09-2019, 07:09 AM   #1
ddaneels
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Location: Belgium

Join Date: Mar 2012
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Default add UMI sequences to fastq read name

Dear all,

I have paired-end fastq data generated with Illumina bcl2fastqv2.19 & sequenced on a Novaseq.The i5index is 7bp long, the i7 8bp long

R1.fastq.gz contains R1 101bp reads:

Code:
@A00154:125:HGKTMDMXX:1:1101:10420:1000 1:N:0:AACTGAGG+ATGCGTC
CTGGCCGTCTCAGCCGAGAAGCCGAGGATTGAATGGGCATGGAGACTGAACTACCCCTCTCACCTTTAGAGGTGGCTCCTCCAAGTCGGGGTTGACGCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
R2.fastq.gz contains 6bp UMI sequence

Code:
@A00154:125:HGKTMDMXX:1:1101:10420:1000 2:N:0:AACTGAGG+ATGCGTC   
GCGCGT
+
FFFFFF
R3.fastq.gz contains R2 101bp reads:

Code:
@A00154:125:HGKTMDMXX:1:1101:10420:1000 3:N:0:AACTGAGG+ATGCGTC
CTTCATAGGCCACAAAAAGCCCATATATCAGTGTCATCCACTAAGCCTCAGACACTGCAGCACGGGCAGCGGCAGTGCCAGCTTCGCCCACACTGCCCCTC
+
FFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
In a downstream analysis I want to use UMI-tools for deduplication. However for that I need the UMI be part of the read name. @Instrument:RunID:FlowCellID:Lane:Tile:X:Y:UMI ReadNum:FilterFlag:0:IndexSequence or SampleNumber

There are tools to add a UMI to the read name when the UMI is present in the read itself. But in my case, the UMI is in a seperate fastq. How could this be achieved?
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Old 01-09-2019, 03:07 PM   #2
GenoMax
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Posts: 6,854
Default

Cross-posted and answered on Biostars: https://www.biostars.org/p/357359/#357497
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demultiplexing, fastq, umi

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