Problems with sra to fastq conversion with 454 reads

[allivi]

Hi,

I am tryind to convert SRA(ftp://ftp-trace.ncbi.nlm.nih.gov/sra.../SRR024155.sra) with paired end reads to fastq with

fastq-dump --split-files SRR024155.sra

It generates two files of size 16Mb and 145Mb. Reads in the first file have length of 4. Is seems obviously wrong. Does anybody know right way to convert SRA with paired end 454 reads to FASTQ?

Thanks.

[irisxkx]

Hi,
I am wondering why did no one post an answer to this question? Was it too stupid of a question? I hope not, because I have the same question... I would appreciate any guidance since I don't have the time to read whole manuals only for extracting a set of reads from SRA.

Thanks,

[WhatsOEver]

Hi,
the "--split-files" parameter gave also sometimes weird outputs for me. Try to use

fastq-dumb --split-3 yourSRAfile.sra

This way 1 file will be generated for single end data, 2 files (with sufffix "_1" and "_2") for paired ends and 3 files (suffix "_1", "_2" and w/o suffix) if there are reads without mate pairs.