I've read the threads out there but haven't been able to solve this problem.
I am trying to separate a paired end sra formatted file to the corresponding two fastq mate pair files.
I've used both:
fastq-dump --split-files MyFile.sra
fastq-dump --split-3 MyFile.sra
The output consists of 2 files, but one of the files has a read length of 75, while the other has a read length of 9. Obviously, not working correctly.
Here's what it looks like:
@SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=75
NTCGTTACAATATCCACCCTGTCCCCGAAGAATGCTCTTGNNNAGNNNNNNNNNNNNNNNNNTNNNNNNNNCTNA
+SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=75
#))))+++(*7AAAAAA75A33303AAAA##############################################
@SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=75
NCGCGTTCCGAAGCCATTTTCATCAAAATCTCGTGAAAAANNNATNNNNNNNNNNNNNNNNNANNNNNNNNTTNG
+SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=75
#++('+****5AAA83353.3388803.35AAAA#########################################
@SRR514860-split_test.3 SOLEXA3_0001:5:1:1024:19859 length=75
NGCGCCCCCTGTGCAGAGGTACTATTGCTGCTGCTGCTGCNNNTGNNNNNNNNNNNNNNNNNANNNNNNNNACNG
==> SRR514860-split_test_2.fastq <==
@SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=9
NNNNNNNNN
+SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=9
#########
@SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=9
NNNNNNNNN
+SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=9
#########
@SRR514860-split_test.3 SOLEXA3_0001:5:1:1024:19859 length=9
NNNNNNNNN
Has anyone run into something similar before? Could this be due to the way the file was submitted and not necessarily the sra toolkit?
Thanks,
John
I am trying to separate a paired end sra formatted file to the corresponding two fastq mate pair files.
I've used both:
fastq-dump --split-files MyFile.sra
fastq-dump --split-3 MyFile.sra
The output consists of 2 files, but one of the files has a read length of 75, while the other has a read length of 9. Obviously, not working correctly.
Here's what it looks like:
@SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=75
NTCGTTACAATATCCACCCTGTCCCCGAAGAATGCTCTTGNNNAGNNNNNNNNNNNNNNNNNTNNNNNNNNCTNA
+SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=75
#))))+++(*7AAAAAA75A33303AAAA##############################################
@SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=75
NCGCGTTCCGAAGCCATTTTCATCAAAATCTCGTGAAAAANNNATNNNNNNNNNNNNNNNNNANNNNNNNNTTNG
+SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=75
#++('+****5AAA83353.3388803.35AAAA#########################################
@SRR514860-split_test.3 SOLEXA3_0001:5:1:1024:19859 length=75
NGCGCCCCCTGTGCAGAGGTACTATTGCTGCTGCTGCTGCNNNTGNNNNNNNNNNNNNNNNNANNNNNNNNACNG
==> SRR514860-split_test_2.fastq <==
@SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=9
NNNNNNNNN
+SRR514860-split_test.1 SOLEXA3_0001:5:1:1024:2576 length=9
#########
@SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=9
NNNNNNNNN
+SRR514860-split_test.2 SOLEXA3_0001:5:1:1024:6017 length=9
#########
@SRR514860-split_test.3 SOLEXA3_0001:5:1:1024:19859 length=9
NNNNNNNNN
Has anyone run into something similar before? Could this be due to the way the file was submitted and not necessarily the sra toolkit?
Thanks,
John
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