I'm trying to get my SE colorspace dataset from SRA (SRR040361) to work. SRA datasets apparently have an extra quality value which Tophat doesn't like, so I deleted the first character of each quality string.
That still led to an error message from prep_reads. So I'm trying with very small files & my very rusty C++ knowledge to probe prep_reads. Which leads to a very weird response
With only one sequence in my file
With two sequences (the same ones!)
With three
Etc.
Here is the table:
BTW, the URL http://randspringer.de/bam referred to in a config error message does not exist
That still led to an error message from prep_reads. So I'm trying with very small files & my very rusty C++ knowledge to probe prep_reads. Which leads to a very weird response
With only one sequence in my file
Code:
Error: qual length (1) differs from seq length (51) for fastq record SRR040361.2
Code:
Error: qual length (9) differs from seq length (51) for fastq record SRR040361.2
Code:
Error: qual length (17) differs from seq length (51) for fastq record SRR040361.2
Here is the table:
Code:
#seq rpt len 1 1 2 9 3 17 4 33 5 41 6 49 7 52 8 52
BTW, the URL http://randspringer.de/bam referred to in a config error message does not exist
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