Question: Error while mapping reads to assembly using bowtie
1
gravatar for Biocode_user
3.4 years ago by
Biocode_user10
Sweden
Biocode_user10 wrote:

I am trying to map assembly back to the reads using bowtie. But with one of the libraries, i get an error

Error:

Warning: skipping mate #2 of read 'DHKW5DQ1:246:C1D7AACXX:4:1101:7855DDDDDDDDDD@BCEEDDDDDDD5AGAAGAAGTCDACADECCDTGGGCGCC' because length (0) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'DHKW5DQ1:246:C1D7AACXX:4:1101:7855DDDDDDDDDD@BCEEDDDDDDD5AGAAGAAGTCDACADECCDTGGGCGCC' because it was < 2 characters long
Error: Read ;GTT has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)


Could anyone please help me to know .. What exactly is the problem with this?

rna-seq assembly • 3.8k views
ADD COMMENTlink modified 3.4 years ago by Antonio R. Franco4.0k • written 3.4 years ago by Biocode_user10

you seem to have a problem with your fastq file. You should take a look at it. Especially at the read named in the error message. Try:

grep -C 4 'DHKW5DQ1:246:C1D7AACXX:4:1101'
ADD REPLYlink written 3.4 years ago by nterhoeven80
1
gravatar for Antonio R. Franco
3.4 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:
Error: Read ;GTT has more read characters than quality values

Take a look to this Wiki on fastq files to learn what is happening. The number of bases within a same read and its ascii values indicating the quality of these bases must be identical

Another problem can raise. If using paired data, sometimes after a trimming you erase the mate read. Some programs expect to find both, the main read and its mate 

In addition.If you compare this read shown below with that shown in the wiki, you will notice that after the positional indication of the read (4:1101:7855), you have letter corresponding to the quality (D and E and @ are not bases), and then it comes the base sequence itself. I don't know where you got this, but this is not a regular fastq read ​ ​

DHKW5DQ1:246:C1D7AACXX:4:1101:7855DDDDDDDDDD@BCEEDDDDDDD5AGAAGAAGTCDACADECCDTGGGCGCC' 

 

ADD COMMENTlink written 3.4 years ago by Antonio R. Franco4.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1124 users visited in the last hour