The fastq file contains empty short reads

[GoogleCodeExporter]

I generated some fastq file and found there are many empty short reads;
I don't know if it is known issue or a new bug.
Please see the second read, no read and quality strings.

===========================================================================
@chr1:136095799-136134196C:U021783-1:3:4997:4211:5108:5059:5108
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+
ab`]aaa_baBba]a[_\\a[aa]_IRTa_aabaJ\b[aaab\`SVBaa_
@chr1:136095799-136134196C:U021783-1:4:4997:5108:5151:5108:5151

+

@chr1:136095799-136134196C:U021783-1:5:4997:3145:5211:5162:5211
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+
B_ab]aNba_`O\Za^a\aJabaa^]aba\_\b]_ab^``a_a\Wa\b]\
===========================================================================

Original issue reported on code.google.com by Guorong...@gmail.com on 14 May 2010 at 10:05

Attachments:

• P1.zip

[GoogleCodeExporter]

Hi Xu,

thanks to all the information you attached, I could rather quickly reproduce the
problem: reads that appeared empty are from polyA/polyT cDNA fragments shorter 
than
the read length (50nt in your case). The sequencing module currently does not 
include
sequences of adaptors and primers that are ligated to the cDNA molecule before
sequencing, therefore reads from fragments that are shorter than the readlength 
are
truncated, here the corresponding thread I created in the Flux Forum:

http://fluxcapacitor.wikidot.com/forum/t-241978/truncated-reads

Truncation of reads from polyA cDNA was buggy and resulted in a read length of 
0.

Original comment by gmicha@gmail.com on 16 May 2010 at 8:15

• Changed state: Accepted
• Added labels: OpSys-All, Simulator

[GoogleCodeExporter]

Bug fixed in build 20100516.

Original comment by gmicha@gmail.com on 16 May 2010 at 8:16

• Changed state: Fixed