[Bioperl-l] barcode split a paired-end fastq file

[Matthew McCormack]

Thank you for your reply, Paul.

Here is the first 18 lines of my fastq file (strangely enough it seems 
to have missed the quality coding line for the first sequence. However 
the last line of this file is a single quality code line), and below it 
are the barcodes.

@M02850:116:000000000-ANY8B:1:1101:12375:1762 1:N:0:1
CATGTAATTCAAAATCCAATAAATCAAAAATAAAAAAAATCAAAAAACAAAAAACTAATCAACATATTAAACTTTCCAAATTCATTAACCAAAAACTAATCTCACTTCTCACAAACCACATCAACTTTCTTCATTCTTCAAT
+
FFFGFGGGGGGGGGHHHGHHHHHHCFHHHHHHGHHHGGGHHHHGHHGGHHHGHGGHHHHHHHGHHHHHGHHHFHHHHHHHHHHHHHHHHHFHHHFEFHHHGHHHHHHGHHHBGHHGGHGHHHHHHHHHGHHHHHHHGHHGHF
@M02850:116:000000000-ANY8B:1:1101:12375:1762 2:N:0:1
CATGGTGTAAATAGTTTAAAGTATTGTTATTATGTTTATTTTTGTATGGTTTTTGGAAATTGAGAAAGAGGAGAATTTAAAGAGGATGTGTGAGAGAGATAGTTTGATTTTTTGATTGAAGAATGAAGAAAGTTGATGTGGT
+
FFFGGGGGGGFGGHGHHHHHHDGGHHFHFHHHHHHGGFHHHHHCGHHHHHHHGGGGFHHHHGFHFHHFFGHHGEGHHHHHFFGGHFHHHFHHBFGFFEFHHHHHHGHHHHFHGGAGHHHHHFGHHHHGHGHHFHFHHFGHFG
@M02850:116:000000000-ANY8B:1:1101:18019:1825 1:N:0:1
ATTCGAGAATCTCATATATTCTTTATCGAAACCCATACATCTTTCCGTCGAAAATCTCATATATACCTTATCCCATTCAACATTCATACGAACGCCGCTCTAGAATTTTTACTTTTCGCCATTAATCCAAATACTATTTAAT
+
FFFGGGGGGGGGGHHHHHHHHHHHHHHHHHGGHGGHHHGHHHHHHHGHHGGGGGHHHHHHGHHHHHGHHHHHHHHHHHHHHHHHHHHHHHGHGGGGGGGGHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHH
@M02850:116:000000000-ANY8B:1:1101:18019:1825 2:N:0:1
TGGAAAAAATAATAATAATTTGATTGTTAGTATTTTATAAATCGATAAATCGTAAGAAGAAAAATATAAAAATAATATTAAAGTTGTGTGCTAAAAGCAATTTTAAATAATTAAATAGTATTTGGATTAATGGCGAAAAGTA
+
FFFFGGGGGGGGGHHHGHHHHHHHHHGHHHHHHHHHHHHHHHGEHAGGHHHGFHHHGHHHHHHGHHHGHGHHHHHHHHHHHGHHHHHGHHFHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGGHHHHHHGGFGGGFHHH
@M02850:116:000000000-ANY8B:1:1101:16147:1845 1:N:0:1
AATATATTAATATTAAAGAGTTATGGGTTGGAGTTTATATATTTTTTCGTCGAGAATTTTATATATATTTTATTTTATTTAATATTTATACGAGCGTCGTTTTAGGGTTTTTGTTTTTCGTTATTGGTTTAAGTGCTATTTG


FWABisF0    TATA
FWABisF1    CATA
FWABisF2    GATA
FWABisF3    GGTA
FWABisF4    CGTA
FWABisF5    AATA
FWABisF6    AGTA
FWABisR1    ATTC
FWABisR2    ACTC
FWABisR3    CATC
FWABisR4    CCTC
FWABisR5    TATC
FWABisR6    TCTC
WRKYBisF1    CAAG
WRKYBisF2    GTAG
WRKYBisF3    GGAG
WRKYBisR1    ACTG
WRKYBisR2    CATG
WRKYBisR3    TATG

Matthew

On 5/25/2016 7:32 PM, Paul Cantalupo wrote:
> Hi Matthew,
>
> I'm not sure about any Bioperl modules (hopefully somebody else will 
> chime in). But there are several routes for help on this matter.
>
> 1. Reply back to this message showing enough of your sequence file and 
> your list of 8 barcodes so we can provide further advice.
> 2. Post your question to http://stackoverflow.com/. Here though, you 
> want to make sure follow guidelines found here 
> <http://stackoverflow.com/help/mcve> and here 
> <http://stackoverflow.com/help/how-to-ask>.
> 3. Post your question to https://www.biostars.org/ 
> <https://www.biostars.org/>. They probably have similar links for how 
> to ask a good question like stackoverflow but I do'nt have the links 
> for them.
>
> Paul
>
>
> Paul Cantalupo
> University of Pittsburgh
>
> On Wed, May 25, 2016 at 4:08 PM, Matthew 
> <mccormack at molbio.mgh.harvard.edu 
> <mailto:mccormack at molbio.mgh.harvard.edu>> wrote:
>
>     Are there any BioPerl modules that would help to split a barcoded
>     fastq file ?
>
>     I have tried FASTX-toolkit, but it does not work on paired-end data.
>
>     The file I have been given is paired-end but a single file, and I
>     have a list of 8 or so 4 letter barcodes.
>
>
>     Matthew
>
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