Can you share the first hundred lines of the FastQ files you retrieve from EBA SRA and NCBI SRA? Alternatively, you can check yourself to ensure the reads are formatted the same way. One known issue with the NCBI SRA Tools wrapper is that it imports paired end data as one FastQ file. This could skew your analysis if the paired reads are not split.
Cheers, Mo Heydarian
I apologize for being so persistent with this, but there is still an issue with the uploads. The extract files tools allows me to upload samples however, when I test those against the samples already run, they yield completely different results. For instance, where I would use Bowtie and get 1.58% (Get Data>uploads from EBI SRA sequences) alignment, I would get 0.00% alignment (NCBI SRA tools> Extract files). This is a HUGE margin given the nature of my research.
I am using the main galaxy at usegalaxy.org. All imports fail to upload.
Unable to fetch ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR102/008/SRR1027188/SRR1027188_1.fastq.gz: [Errno 104] Connection reset by peer
Fatal error: Exit code 2 () /galaxy-repl/main/jobdir/014/658/14658998/tool_script.sh: line 9: [: SRR1027188: unary operator expected
Above are the error codes I continue to receive. The top error message from Get Data, EBI SRA the second from EBI SRA Extract.
I'm so disappointed that I haven't been able to run any samples for several days now.
Please fix as soon as possible.