input format?

[Nats Timoneda]

Hi everybody,

I have files from Illumina Miseq Nextera, in fastq format and I will try to use SolexaQA,
and I have 2 problems:
1: Warning: Desired sample size (10000) greater than number of sequences per tile
2: the program not recognize my fastq format :

  Use of uninitialized value $qual[0] in hash element at SolexaQA.pl line 560, <INPUT> line XXXX

Tanks in advance,

Natàlia

[MPC]

Hi Natàlia,

The first warning indicates that there are fewer than 10,000 reads per tile.  Given that a current MiSeq run should produce about 15m reads per lane, this is a bit surprising.  Are you running large numbers of barcoded samples?  Or do you have any indication that the run may have failed?

The second error suggests that your FASTQ file may not be in a standard format.  Could you please send me, say, the first 1000 lines?  I'll take a look and see if I can figure out what's going on.

Best

-Murray