#310 Incorrect fastq format of --un output

v0.9.0
closed
Val
None
5
2014-12-01
2014-05-12
Raimi
No

Hi,

I was trying to use bowtie2 in order to clean PacBio data from its spike in. So any read that do not aligned to control read (i.e. --un) are the one look for. However, the output of this is not in the correct format and that the @m* are in the same line as the quality line:

+
)--'(%')+'#$$$&'.-(/.-)%#).&..+-/--.#+#,,%,-+"'(.%(&&$#%&&$#')((\ '''&.)--+)/+/..'+.///.(#-,,///.././.,./&/-0-++//--.+//.//(//"..@m140123_0532

But this is not for all reads only some of them are like this and some of them would have the quality value missing or shorter than the read base.

Thank You

Discussion

  • Val

    Val - 2014-07-31

    Hi Raimi,

    Can you please download the source code from here: https://github.com/BenLangmead/bowtie2/archive/master.zip

    Please let me know if this solves the problem you are having.

    thanks,
    Val

     
  • Val

    Val - 2014-12-01

    I assume the suggested download solved the problem.

    Val

     
  • Val

    Val - 2014-12-01
    • status: open --> closed
    • assigned_to: Val
     

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks