Question: Fastq Splitter Empty And Fastq Manipulator Doesn'T Work
0
Janice Patterson • 20 wrote:
I am having the same issue as this user:
http://user.list.galaxyproject.org/FASTQ-splitter-produced-empty-
dataset-please-help-td4654388.html
I have a fastq file, in which both paired end reads were concatenated
into a single file.
@HWI-ST632:288:C2L0BACXX:8:1101:1639:1746 1:N:0:GCCAAT
NTTTGTCTCTGGTCTGTACTTGTGGGCCAGCTTAAGCAGCTGAGTAGCTGTTTGGCGGTCCAGGGCCTGG
GTGAACTGGTTAATCGCAGGAGGCACTTTCA
+
#1=DDFFFHHHGFHJIHJIJJIHHJJJIIIIIJJGIGIGIJIGIDGHJIIJJJJJIJJGHHGFFFFDDDD
DCBBDCCDDCDDDEDDDDDDBDDDDBDDCCC
@HWI-ST632:288:C2L0BACXX:8:1101:1876:1741 2:N:0:GCCAAT
NTTTATTTTTCGTTATTGTTGGTGGTTTAAAAAATTCCCCCCATGTAATTATTGTGAACACCTTGCTTTG
TGGTCACTGTAACATTTGGGGGGCGGGACAG
Fastq splitter results in empty data sets because, as explained in the
thread, the data is already split into their corresponding forward and
reverse reads and splitter is meant to split reads in which the paired
end reads have been joined tail to head.
I tried the manipulate FASTQ tool as the thread above suggests,
however the FASTQ sequence identifier is slightly different so the
suggested Match of .1 and .2 example shown in the thread doesn't work,
because my FASTQ file has the identifier in Casava 1.8 format, in
which the identifier line does not end with the 1 or 2 for forward and
reverse strand. Instead the strand is identified as the 1 or 2 after
the space in the identifier line, so <space>1:N:0 . . . and
<space>2:N:0 . . . . I tried running FASTQ manipulator with the Match
Reads according to regular expression with " 1:" and " 2:" but that
did not work, I ended up with two identical fastq files with same
sequences as the original file, so it basically just made a copy and
did not deconcatenate the forward or reverse.
Am I using this Match Reads by regular expression wrong?
Janice Patterson
patterja@ohsu.edu
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modified 4.9 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
4.9 years ago by
Janice Patterson • 20
