Several .lite.sra files I downloaded from the SRA are giving me problems when I try to extract the paired-end fastq files. If I use any of the splitting functions of fastq-dump (--split-files or --split-spot), I get a forward read with length 76 and a reverse read with length 216 when I should be getting 146 for each. Does anyone know how to force fastq-dump to split the spots at a given length? Or is there another tool that could be used to fix the malformed reads?
For example: SRR306633.lite.sra
fastq-dump --split-files SRR306633.lite.sra
head *.fastq
==> SRR306633_1.fastq <==
@SRR306633.1 HWI-EAS66_0013_FC6270K:8:1:1351:1043 length=76
GAGTTGGTCCACGCGAATACTTGACCGTATAAACTTGGTCTGCCCACATTTATTTGCTGCCATTTGTTACGTTTGT
+SRR306633.1 HWI-EAS66_0013_FC6270K:8:1:1351:1043 length=76
B,DBDDDDB:BBB@DDDD8:DD4D;DDDDD@DDDB9DD;;BB1>*<44?2DDD@DDBDDD0<3BDBB;>)?>>;>D
@SRR306633.2 HWI-EAS66_0013_FC6270K:8:1:1660:1041 length=76
CTTGATGCAAAATCCTTTTTTGATTTACCTACAATTACTAAGTATTTCTCTCAGTGTAGCCATAAACAGCACGAAA
+SRR306633.2 HWI-EAS66_0013_FC6270K:8:1:1660:1041 length=76
GBD8DBDGGBGFG@G>GCGBH>H=F3BEDEE?:GDGDGGGDGDGEEEGGGGG:>GEBDBE84FEFGG@G-B3DBD4
@SRR306633.3 HWI-EAS66_0013_FC6270K:8:1:1929:1038 length=76
TTGTATTTTTGGTTCTACACTGNACTTTTAATTTGCGCAAATAATTGATTATTCAGCAATTTTCTTACCAATTTGA
==> SRR306633_2.fastq <==
@SRR306633.1 HWI-EAS66_0013_FC6270K:8:1:1351:1043 length=216
TTATCCTGGCTGGGGAATCCTTGATGTCAAACTACTANNCTTGTTGACTTTTTTTATGGGTNTTATTCAGCATTCAAAATTAAANNNNNNNNTCGTATTCCTGATTNGAATGACCAGTCAAGTCATTNTGATAGTATTTTTTTTTCGCAGTGCCTTGCAGTACTTGTGCCCAGNNNNNNNNNGCTGTACTGACATATNNNNNNTGGCTTTTACTTG
+SRR306633.1 HWI-EAS66_0013_FC6270K:8:1:1351:1043 length=216
D:)DB#################################################################F:DG@GGG?G98,,########6=65==9>E4CFEB#BB=:=567,@@@=<GE?G,8#A?8B?B=F3EC@AAAAA>4><EEDE8F<FGDGG:DE-:DD2D5;@#########8@>?:4,AE@-8?#####################
@SRR306633.2 HWI-EAS66_0013_FC6270K:8:1:1660:1041 length=216
AGCACTTGACGGCAATGAATTCTGACACACGTGTGCCNNCCACCCAAACTTCCCGACCGCNNCCCTCGCCAAAAAGTATAAGGNNNNNNNNNNCGGAATACAGTCCNTANNATGCGNNTTAATCTCCNACTTTTATGTTCATCCAAAGGTGGTGCACACGAACCACTGGCGCCNNNNNNNNNGGCTGCTGTAGCCCTNNNNNNAGAATCGGTCACA
+SRR306633.2 HWI-EAS66_0013_FC6270K:8:1:1660:1041 length=216
=B3=?C6=?)?CA=BDB3,DBDBD3?+<BA::A#####################################G?GEGDC3FG=:=##########:;8:1?:EEGG<@#AA##=@@,>##8==;B8@?D#DBFFEDFDA2GB@=5==BAFE-E4EB2AA>+G??@D####################################################
@SRR306633.3 HWI-EAS66_0013_FC6270K:8:1:1929:1038 length=216
ATGTTTTGAATGTTCTTTGAATGTTTTACGTAGGCCTNNATGTAAACTGCCTGCTTATTNNNTGTCATTTTTCTACTCCAACANNNNNNNNNNGNAGCTCGACTTANTTNNAAACANNTGTTGTTANNNAGCTGATCTCGATATCTATTTTGATTATCCCCCACCCAGAAGTANNNNNNNNNCTTTAAAAAATATGNNNNNNNTTTAAAAAAACAT
Thank you!
as a workaround have u tried to download the files from ddbj http://trace.ddbj.nig.ac.jp/