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How to split Illumina Hiseq 2000 paired-end fastq files?

Hello,

I have several paired-end .fastq files that I would like to run through Kallisto. However according the Kallisto's manual :

The default running mode is paired-end and requires an even number of FASTQ files represented as pairs, e.g.

kallisto quant -i index -o output pairA_1.fastq pairA_2.fastq pairB_1.fastq pairB_2.fastq"

My .fastq files are already paired, and the following shows the first several lines:

@HISEQ2000:404:C73LWACXX:2:1101:1487:1876 1:N:0:CGATGT

NCCCTCTTGAACTCTCTCTTCAAAGTTCTTTTCAACTTTCCCTTACGGTACTTGTTGACTATCGGTCTCGTGCAGATCGGAAGAGCACACGTCTGAACTC

+

#4=DB?:DF?ADCFFGD>BHCEB9F3AAACEFHC>@BBFFFGD@??BF??D9B?FGDFFGDGGB@;AE>ED25;)..;;=;=>;;(;=@?B2?9@:(:AB

@HISEQ2000:404:C73LWACXX:2:1101:1355:1989 1:N:0:CGATGT

GGCAGATAGGAAGTGTCCAGAAGCTGGGCCACGGCAGCCTTCAGCTCTCGGGCGTCCTCGGGGCTGGGCTCTAGAACCGGAAAGCCACGCTCCTCCTCCN

+

@@@DDDD?DFFDF<A2<<EC@;G@AFBDEECB0CA@G7B39??DA4==8;FF@EBB?;@@>?B=/5>B@B@B@BB>4259-998?###############

@HISEQ2000:404:C73LWACXX:2:1101:1738:1959 1:N:0:CGATGT

ACGCCCGGCTGCAGGAGCCATTCTAAGTTTCCCAGATTTCCTTCATGGTCACTATTTACCTTTTGTTTGTTTGTTTTTTTGCGTTCGAGACAGGGTTTCT

+

B@@FFFFFHHHHHJJIIJJJJJIJJJFIIIJIJJIFGHIIIJIJJIJFHIIHJJJIGEGGIIIJJHEHHHHFFFFBCDDDBABBDB@ACBDDD<?<<BCD

@HISEQ2000:404:C73LWACXX:2:1101:1679:1997 1:N:0:CGATGT

GCTTACTTTAATACCTTTTTAGGGTTTGCTGAAGATGGCGGTATATAGGCTGAATTAGCAAGAGATGGTGAGGTAGAGCGGGGTTTATCGATTATAGAAC

+

CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJIIJJJJJJJJFGIIJIJJIJJJJJJJIJJIJFFHHGFCDCDE;@>ACDDDDD5<<C@CDD?CDADCCD#

@HISEQ2000:404:C73LWACXX:2:1101:2016:1976 1:N:0:CGATGT

GTCCTCTGTGCACATTCTCCATGGCCGCAACCTCAGCCAGTGCAGCGAGGCTGAAGAACGCAGACACAGCAGGCATGTCTGGAGTGCTGCTCCGTGGCAG

+

CCCFFFFFHHHHGEIJJJJJJJIIJJJJIJJJJJJIJJJJIIIJJJJIIJJIGFEHHFFFDDDDDDDDDDDBDBD@ACCEC<CB@ADEDDDCDB?BDDC@

I am assuming that the + sign separates each right/left pair? But how would you then go about splitting them up?

Thanks in advance,

rna-seq fastq paired-end illumina hiseq 2000
• 3,383 views • link
updated by ATpoint ATpoint • written by Yuka Takemon • Yuka Takemon

1 answer

The data you show here is only displaying the forward pairs, and presumably you have a file named something like "_r.fastq" or "_2.fastq" with the reverse pairs. If not, you might want to check your data source to see that you have all the files or maybe check the end of the file to ensure the reads were not concatenated naively.

• 0 views • link
written by SES SES

Thanks I realized that I only downloaded 1 of 2 files! oops!

• 0 views • link
updated by Ram Ram • written by Yuka Takemon • Yuka Takemon

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