split-by-adapter does not modify the quality header

[korneel-emweb]

I noticed that when a read is split because there is an adapter in the middle, the name gets changed to "split-by-adapter....". But I am working with a file that repeats the read name on the quality header (so "+readname" matching "@Readname"). The fastq spec requires these names to be the same, which is no longer the case after the "split-by-adapter" gets added. There is a downstream tool that is complaining about this in my workflow.

Not a major issue, but I thought I'd mention it.

[sfchen]

can you please show me some FASTQ lines as an example?

I think the FASTQ spec requires every read has an unique identifier.

[korneel-emweb]

Yes of course, that's a great idea, I should have included it from the start 😅

As you can see below the name after the "@" is different from the name after the "+".

@split-by-adapter-left-SRR31023696.64 48f67eb3-b2ec-43fe-89e7-4d104989ea5b length=427
CCTAAAGGAGACACCGAGAATCCCAGAATCAAGACTCATCCAGTGTCCATCATGGGTCTCAAGGTGAACGTCTCTGTCATAGTCATGGCAGTACTGTTAACTCTAGAACACCAACCGGTCAAATCCATTGGGGCAATCTCTCTAAGATAGGGGTGGTAGGGATAGGAAGTGCAAGCTACAAAGTTATGACTCGTTCCAGCCATCAATCATTAGTCATAAAGTTAATGCCCAATATAACTCTCCTCAACAACTGCACGAGGGTAGAGATC
+SRR31023696.64 48f67eb3-b2ec-43fe-89e7-4d104989ea5b length=427
786544345544432000/100011776331113244332334552223241012146564333344320000167442///./0112254/.../010//123+**+,-655...-/101220000/1000333333345887664100005555000//2/////22233344444443343222////,))*+.24454332213222211211111122211233567320//0034667754321122342.....11111322

[sfchen]

Got it, so I should modify the third line as well if it's not just a +