[lac302]

See this: http://seqanswers.com/forums/showpos...36&postcount=7

BTW: SRR639124 appears to be a single end dataset irrespective of what the SRA record says (this type of thing happens at times).

There must have been an issue with the original submission. The paper this data is based on states that all the runs were paired-end.

[GenoMax]

--split-files option does not seem to be generating the correct files either for SRR639124.

Grab the fastq files from EBI: http://www.ebi.ac.uk/ena/data/view/SRR639124 hopefully they are correct over there.

Note: Even the EBI version has only 1 base in "paired" file.

@SRR639124.1 LEOPARD:627RGAAXX:4:001:00932:10203:0:1/2
N
+
B

At least it is consistent with the SRA record (that says 100 x 1): http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR639124

It is useful to let SRA tech support know when you find records that do not seem to have the right downloads associated with them.

[GenoMax]

EBI may not have the right files either for all (here is an example: http://www.ebi.ac.uk/ena/data/view/SRR639239 says PAIRED but there is only one file).