FASTQ importing

import

#1

Hi all,
I had some help previously on getting an already QCd/primer/barcode trimmed fasta file into QIIME2, this worked well and we’re working away happily on this. In the meantime I was able to get the FASTQ from the folks who originally carried out our sequencing. These again don’t seem to be raw reads, but have come as a single adapter trimmed fastq with (I presume) R1 and R2 reads joined:

@100_1 469 424 24 21 0 0 1
TGAGGAATATTGGTCAATGGACGCAAGTCTGAACCAGCCATGCCGCGTGCAGGATGACGGCTCTATGAGTTGTAAACTGCTTTTGTACGAGGGTAAACGCAGATACGTGTATCTGTCTGAAAGTATCGTACGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG
+100_1 469 424 24 21 0 0 1
[email protected]@[email protected]?CEGGGGFFFFEFGGCFGFGGFGEFEAFFGGGGGDFGFGGEGGGGGGGG5,AFGFGFGGGFC9>[email protected][email protected]@@FFGFFG?ECFGGCCCF8CCC:E*>FIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII[email protected]:GGGGGGGCCFFGGGGGGGGEDCGGFEDGGGGGGEGGFGGGEGGGGGFGFFAGGGGGGGGGGGGGGGGF<GGGGFGF9GFGGGDGFGGGGGGGGGGGGGGGGGCGGGGGGEGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
@100_2 450 405 24 21 0 0 1
TGGGGAATTTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGCGGGACGAAGGCCTTCGGGTTGTAAACCGCTTTCAGCAGGGAAGAACCGAGACGGTACCTGCAGAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGAGAGCGTTATCCGGATTCATTGGGCGTAAAGCGCGCGTAGGCGGCCGCCTAAGCGGAACCTCTAATCCCGGGGCTCAACCCCGCGGCCGGGTTCCGAACTGGGCGGCTCGAGTGCGGTAGGGGCAGGTGGAATTCCCGGTGTAGCGGTGGAATGCGCAGATATCGGGAGGAACACCGATGGCGAAGGCAGCCTGCTGGGCCGACACTGACGCTGAGGCGCGAAAGCCGGGGGAGCGAACAGG
+100_2 450 405 24 21 0 0 1
GGGGGGEGGGGGGGGGCCGGGGGGGGGGGGGGGGGDGGGGGEGGEGGGGDFGGGEGGGCDFGFFGGGGGGGGCFGGGGG:FGGGCGFGGGG<>[email protected]:7<:FGGGG><FGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIEIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIEGEGGGGFGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGFGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGG
@100_3 449 404 24 21 0 0 1
TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAGGAAGAAGTATCTCGGTATGTAAACTTCTATCAGCAGGGAAGATAATGACGGTACCTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCGGAGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACGGCTTTTGAAACTGCCCTGCTTGATTTCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGACAATGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
+100_3 449 404 24 21 0 0 1
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

So I seem to have sample ID, followed by an underscore and some information I do not understand :slight_smile: , so my question is will this file be appropriate for use with the “fastq manifest” import? Even though a) everything is in a single file and b) the read IDs contain this extra information.

Thanks for your help!!


(Nicholas Bokulich) #2

(Matthew Ryan Dillon) #3

If I am understanding you correctly, you have two FASTQ files (one fwd, one rev), that are multiplexed, where the barcodes have been removed, and the sample ID is in the header? If so, unfortunately, we don’t have a tool for that in QIIME 2. If you can find a way to demultiplex these reads, then you can import into QIIME 2 using the manifest format. Sorry! :qiime2: :t_rex:


(Matthew Ryan Dillon) #4

(system) #5

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