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SRA fastq modify by 10x valid fastq

Hi guys,

I have a paired end fastq file with header like this:

@SRR8117283.1.1 1 length=84
GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTATCGGAAGAGCACACGTCAGAACTC
+SRR8117283.1.1 1 length=84
FFF,F:FFF:::FFFFFFFFFF:,FFFFFFFFFFFFFFF,F:FFF,F,F:FF:FF:F,,:,:F,FFFFF,F,,FFF,FFF,:F:

And

@SRR8117283.1.2 1 length=100
CCCTAACCCTAACCATAACACAAACACAAACCCAAACCCAAACCCAAACCAAAACACACACCAAAACCACACCAAAAAACAAAACCCTAACACAAACAAA
+SRR8117283.1.2 1 length=100
,FF,,FFFF:FFF:,,F::,:F::,,,F,,,,,F,:,,,F,:F,,F,,,F,F,FF,,F,,,,F,:,,,:,F::F,F:,,:::F:F,F,F:,,,,:,,:,,

In order to run CellRanger DNA pipeline for alignment, how should I modify the header? Right now I got invalid read Qname from CellRanger DNA.

fastq
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written by wyuan37 • wyuan37

1 answer

Have you created file names as noted in this application note: https://kb.10xgenomics.com/hc/en-us/articles/115003802691-How-do-I-prepare-Sequence-Read-Archive-SRA-data-from-NCBI-for-Cell-Ranger

You could also download the original 10x BAM file uploaded for this dataset (available under Data Access tab here: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR8117283&display=data-access ) and convert using directions provided here: https://kb.10xgenomics.com/hc/en-us/articles/360035250172-Why-do-I-not-see-any-FASTQs-or-incomplete-FASTQs-for-the-SRA-of-my-interest

• 0 views • link
written by GenoMax GenoMax

Thank you! The Data Access is really helpful!

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written by wyuan37 • wyuan37

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