Open paulzierep opened 1 month ago
We discovered, that fastq files downloaded from NCBI SRA via fasterq_dump are different to the ENA stored fastq files. After some digging, this is probably due to the --clip option.
--clip
Example downloaded from: https://www.ebi.ac.uk/ena/browser/view/DRR010705
@DRR010705.1 HUMWT9A01AC2YA/4 ATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGTATTCCTTGGAGCATGCCTGTTTGAGTATCATGAGCAAATCTCAAAGTCAATTCCTTAATTGGTTTTGCTTTGGACTTGGAGGTCTTGCAGATTTCACAGTCTGCTCCTCTTAAATGCATTAGCTGGATCTCAGTAATTATGCTTGGTTCCACTCGGCGTGATAAGTATCACTCGCTGAGGACACTGTTAAAAAGGTGGCCAGGAAATTACTGATTGAACCGCTTCTAACGGTCTATTAAGTTGGACAATTGACCCCTTAAGTTTGATCTCAAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCTTAGTAACGGCGGGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCTTTCAGGGTCCGAGTTGTAATTTGTAGAAGT + EIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHFIIIIIIIIIIIIIIHBBBHDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHCCEECCBBIIIIIIIIADDIIICCEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDCHIIIIIIIIIIIIIIIIIIIIIIHDAADDIIAAA;;AAIAADDACIIAAAA@IIICCAECCICAAACAAAAIBBBBA>>>??@????AA899999;@;;????A?87777<A=:666=<<<;444;<AB996=;AA<<99999<?==;;;8331021..,,,..0..,,,//000.,,,,//1////1186/...1353;8<:7733357:8:777555544841111233310011464333331101440,,,,,.-444221
Default download via fasterq_dump
@HUMWT9A01AC2YA/4 ATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGTATTCCTTGGAGCATGCCTGTTTGAGTATCATGAGCAAATCTCAAAGTCAATTCCTTAATTGGTTTTGCTTTGGACTTGGAGGTCTTGCAGATTTCACAGTCTGCTCCTCTTAAATGCATTAGCTGGATCTCAGTAATTATGCTTGGTTCCACTCGGCGTGATAAGTATCACTCGCTGAGGACACTGTTAAAAAGGTGGCCAGGAAATTACTGATTGAACCGCTTCTAACGGTCTATTAAGTTGGACAATTGACCCCTTAAGTTTGATCTCAAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCTTAGTAACGGCGGGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCTTTCAGGGTCCGAGTTGTAATTTGTAGAAGTAG + EIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHFIIIIIIIIIIIIIIHBBBHDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHCCEECCBBIIIIIIIIADDIIICCEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDCHIIIIIIIIIIIIIIIIIIIIIIHDAADDIIAAA;;AAIAADDACIIAAAA@IIICCAECCICAAACAAAAIBBBBA>>>??@????AA899999;@;;????A?87777<A=:666=<<<;444;<AB996=;AA<<99999<?==;;;8331021..,,,..0..,,,//000.,,,,//1////1186/...1353;8<:7733357:8:777555544841111233310011464333331101440,,,,,.-44422100
It is in fastq_dump. Maybe copy it over?
fastq_dump
bummer: fasterq-dump does not have the clip option
fasterq-dump
We discovered, that fastq files downloaded from NCBI SRA via fasterq_dump are different to the ENA stored fastq files. After some digging, this is probably due to the
--clip
option.Example downloaded from: https://www.ebi.ac.uk/ena/browser/view/DRR010705
Default download via fasterq_dump