add UMI sequences to fastq read name

ddaneels · 01-09-2019, 07:09 AM

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?

GenoMax · 01-09-2019, 03:07 PM

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

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01-09-2019, 07:09 AM	#1
ddaneels Member Location: Belgium Join Date: Mar 2012 Posts: 19	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?

01-09-2019, 03:07 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	Cross-posted and answered on Biostars: https://www.biostars.org/p/357359/#357497