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shendurelab / fly-atac

Code relevant to sci-ATAC-seq of Drosophila embryogenesis.
MIT License
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cell barcode issue #6

Closed jphe closed 2 years ago

jphe commented 5 years ago

Hi,

I have download the SRA file from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111586), and convert it to fastq with fastq-dump. Seems it just like typical fastq file, I can not find where the barcode is.

less SRR6819235.2_1.fastq.gz @SRR6819235.2.1 D00584:151:C9KLUANXX:1:1108:1100:1964 length=50 NTTTTGTTCCCCTTTCTAAGAAGGATCGAAGTATCCACACTTTGGCCTTC +SRR6819235.2.1 D00584:151:C9KLUANXX:1:1108:1100:1964 length=50

<<<<FFFFFFFFFFFFFFFFFBFFFFFF//<FFFBFFFFFFFBFFFF<F

@SRR6819235.2.2 D00584:151:C9KLUANXX:1:1108:1494:1991 length=50 CACATGAACTGGGACTACTTCCTGCTAAGAGAAAGCAGCCAGACATTTAT +SRR6819235.2.2 D00584:151:C9KLUANXX:1:1108:1494:1991 length=50 BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFF/ less SRR6819235.2_2.fastq.gz @SRR6819235.2.1 D00584:151:C9KLUANXX:1:1108:1100:1964 length=50 GAGCTCTGGAGATACTTGTTAGNNNNNNTTGTTTNNNNNNNNNNNNNNNN +SRR6819235.2.1 D00584:151:C9KLUANXX:1:1108:1100:1964 length=50 B<<B////FFB<F/////BFFF######<</<F/################ @SRR6819235.2.2 D00584:151:C9KLUANXX:1:1108:1494:1991 length=50 GTTCTCAGCAACCTCTACTTCCCCTCCCTTTGCCTTTGGTAGAATTTCTT +SRR6819235.2.2 D00584:151:C9KLUANXX:1:1108:1494:1991 length=50 BBBBBFFBF/FFF//</<<FFFBF/BF</<F/B<FFBBFFFFF/<<B/7<

Thanks, Jphe

cusanovich commented 2 years ago

Apologies for not responding sooner. The barcodes should be available from SRA Toolkit if you use the -F argument with the fastq-dump command.