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Thank you for your reply, Paul.<br>
<br>
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.<br>
<br>
@M02850:116:000000000-ANY8B:1:1101:12375:1762 1:N:0:1<br>
CATGTAATTCAAAATCCAATAAATCAAAAATAAAAAAAATCAAAAAACAAAAAACTAATCAACATATTAAACTTTCCAAATTCATTAACCAAAAACTAATCTCACTTCTCACAAACCACATCAACTTTCTTCATTCTTCAAT<br>
+<br>
FFFGFGGGGGGGGGHHHGHHHHHHCFHHHHHHGHHHGGGHHHHGHHGGHHHGHGGHHHHHHHGHHHHHGHHHFHHHHHHHHHHHHHHHHHFHHHFEFHHHGHHHHHHGHHHBGHHGGHGHHHHHHHHHGHHHHHHHGHHGHF<br>
@M02850:116:000000000-ANY8B:1:1101:12375:1762 2:N:0:1<br>
CATGGTGTAAATAGTTTAAAGTATTGTTATTATGTTTATTTTTGTATGGTTTTTGGAAATTGAGAAAGAGGAGAATTTAAAGAGGATGTGTGAGAGAGATAGTTTGATTTTTTGATTGAAGAATGAAGAAAGTTGATGTGGT<br>
+<br>
FFFGGGGGGGFGGHGHHHHHHDGGHHFHFHHHHHHGGFHHHHHCGHHHHHHHGGGGFHHHHGFHFHHFFGHHGEGHHHHHFFGGHFHHHFHHBFGFFEFHHHHHHGHHHHFHGGAGHHHHHFGHHHHGHGHHFHFHHFGHFG<br>
@M02850:116:000000000-ANY8B:1:1101:18019:1825 1:N:0:1<br>
ATTCGAGAATCTCATATATTCTTTATCGAAACCCATACATCTTTCCGTCGAAAATCTCATATATACCTTATCCCATTCAACATTCATACGAACGCCGCTCTAGAATTTTTACTTTTCGCCATTAATCCAAATACTATTTAAT<br>
+<br>
FFFGGGGGGGGGGHHHHHHHHHHHHHHHHHGGHGGHHHGHHHHHHHGHHGGGGGHHHHHHGHHHHHGHHHHHHHHHHHHHHHHHHHHHHHGHGGGGGGGGHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHH<br>
@M02850:116:000000000-ANY8B:1:1101:18019:1825 2:N:0:1<br>
TGGAAAAAATAATAATAATTTGATTGTTAGTATTTTATAAATCGATAAATCGTAAGAAGAAAAATATAAAAATAATATTAAAGTTGTGTGCTAAAAGCAATTTTAAATAATTAAATAGTATTTGGATTAATGGCGAAAAGTA<br>
+<br>
FFFFGGGGGGGGGHHHGHHHHHHHHHGHHHHHHHHHHHHHHHGEHAGGHHHGFHHHGHHHHHHGHHHGHGHHHHHHHHHHHGHHHHHGHHFHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGGHHHHHHGGFGGGFHHH<br>
@M02850:116:000000000-ANY8B:1:1101:16147:1845 1:N:0:1<br>
AATATATTAATATTAAAGAGTTATGGGTTGGAGTTTATATATTTTTTCGTCGAGAATTTTATATATATTTTATTTTATTTAATATTTATACGAGCGTCGTTTTAGGGTTTTTGTTTTTCGTTATTGGTTTAAGTGCTATTTG<br>
<br>
<br>
FWABisF0 TATA<br>
FWABisF1 CATA<br>
FWABisF2 GATA<br>
FWABisF3 GGTA<br>
FWABisF4 CGTA<br>
FWABisF5 AATA<br>
FWABisF6 AGTA<br>
FWABisR1 ATTC<br>
FWABisR2 ACTC<br>
FWABisR3 CATC<br>
FWABisR4 CCTC<br>
FWABisR5 TATC<br>
FWABisR6 TCTC<br>
WRKYBisF1 CAAG<br>
WRKYBisF2 GTAG<br>
WRKYBisF3 GGAG<br>
WRKYBisR1 ACTG<br>
WRKYBisR2 CATG<br>
WRKYBisR3 TATG<br>
<br>
Matthew<br>
<br>
<div class="moz-cite-prefix">On 5/25/2016 7:32 PM, Paul Cantalupo
wrote:<br>
</div>
<blockquote
cite="mid:CAJqbkv5Sk0WyK2sE1wVM89VYiErQTCgYdUwLM6jA3FuszUhEpQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small">Hi
Matthew,</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small">I'm not
sure about any Bioperl modules (hopefully somebody else will
chime in). But there are several routes for help on this
matter.</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small">
<div class="gmail_default">1. Reply back to this message
showing enough of your sequence file and your list of 8
barcodes so we can provide further advice.</div>
<div class="gmail_default">2. Post your question to <a
moz-do-not-send="true" href="http://stackoverflow.com/"><a class="moz-txt-link-freetext" href="http://stackoverflow.com/">http://stackoverflow.com/</a></a>.
Here though, you want to make sure follow guidelines found <a
moz-do-not-send="true"
href="http://stackoverflow.com/help/mcve">here</a> and <a
moz-do-not-send="true"
href="http://stackoverflow.com/help/how-to-ask">here</a>.<br>
</div>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small">3. Post
your question to<a moz-do-not-send="true"
href="https://www.biostars.org/"> https://www.biostars.org/</a>.
They probably have similar links for how to ask a good
question like stackoverflow but I do'nt have the links for
them.</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small">Paul</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small"><br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature">
<div dir="ltr"><span style="font-family:times new
roman,serif">Paul Cantalupo<br>
University of Pittsburgh</span><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Wed, May 25, 2016 at 4:08 PM,
Matthew <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:mccormack@molbio.mgh.harvard.edu"
target="_blank">mccormack@molbio.mgh.harvard.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Are there
any BioPerl modules that would help to split a barcoded
fastq file ?<br>
<br>
I have tried FASTX-toolkit, but it does not work on
paired-end data.<br>
<br>
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.<br>
<br>
<br>
Matthew<br>
<br>
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</blockquote>
</div>
<br>
</div>
<br>
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