fastq file without index?

[lisann_5]

Dear All,

I have a fastq file which failed to align with bowtie. The error message is: reads file does not look like a FASTQ file. I don't know what is going wrong. Is it possible that there is no index in the fastq file? This is how my fastq file looks like:

@D5N3XBQ1:149:C0TCLACXX:2:1101:1342:2245 1:N:0:
TTAATAAAAGCTATTGAT
+
BB**?BHGG9?0?8888B
@D5N3XBQ1:149:C0TCLACXX:2:1101:1583:2228 1:N:0:
ATCGGGCGCAGGGACAGA
+
E99)?0?@6;'5>(;BE@
@D5N3XBQ1:149:C0TCLACXX:2:1101:1688:2238 1:N:0:
GCTGCCCTCCACCATATC



Thanks for all your ideas,

Lisanne

[rahularjun86]

Hi Lisanne,
Have you created the index of reference genome with bowtie2-build? and try to run bowtie with example data (/bowtie2-2.0.0-beta3/example).

Try following commands:

bowtie2-build Genome.fa Genome.build
This will create six new files which constitute the bowtie index necessary for bowtie:

Genome.build.1.ebwt Genome.build.4.ebwt
Genome.build.2.ebwt Genome.build.rev.1.ebwt
Genome.build.3.ebwt Genome.build.rev.2.ebwt

For mapping I used the following commands, Please read the manual and do it accordingly:

bowtie2 -S -q --solexa1.3-quals -p 1 -I 100 -X 600 --fr Genome.build -1 read1.fastq -2 read2.fastq OUT.sam


Thnx

[swbarnes2]

That's weird. Looks like a fine fastq to me, though the quality string is in the old encoding, not the new. Maybe taht's what's confusing bowtie?

You don't index the fastqs. You can index the reference fasta, and you can index a .bam

[kmcarr]

That's weird. Looks like a fine fastq to me, though the quality string is in the old encoding, not the new. Maybe taht's what's confusing bowtie?

Those quality strings are the new encoding; the digits are a dead giveaway that it is Phred+33.

It's entirely likely that whatever bowtie finds objectionable about your fastq file is not represented by the small snippet you have pasted above. I tested the two complete entries you have shown with both bowtie (0.12.7) and bowtie2 (2.0.0-beta7) and it did not generate an error.