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Error encountered using bowtie2 on Illumina fastq file

Dear all,

I am trying to run bowtie 2 on my Illumina file and I receiving the following error:

Error: Encountered one or more spaces while parsing the quality string for read NB50
1124:10:H5LKGAFXX:3:21612:11073:20398 1:N:0:CTTGTN.  If this is a FASTQ file with in
teger (non-ASCII-encoded) qualities, try re-running with the --integer-quals option.
Error: Encountered exception: 'Unidentified exception'

this is a sample of my data

@NB501124:10:H5LKGAFXX:3:11401:20911:1028 1:N:0:
CTTGTANAAATCTCACATTCATAGGGCAGCTCTCCTGAATGTATCAATTCAAGACTTTTGAGATTATCAGAACGTAAGAGCAAACGTATTAAAAACACTCACCTTATTATCTATTATCCAGTATGAATATTTCATAAAAATAAGAGATTGTGGAGGG
+

Thanks for the help,

Cheers

bowtie2 illumina fastq file
• 4,423 views • link
written by ggman ggman

And how does the quality string of read 1124:10:H5LKGAFXX:3:21612:11073:20398 1:N:0:CTTGTN look like?

• 0 views • link
written by WouterDeCoster WouterDeCoster

I checked the quality using Fastqc and it was good. (if this is what you are asking?)

• 0 views • link
written by ggman ggman

I think I found part of the issue with you asked @genomax2, my output looks like this

    @HD VN:1.0  SO:unsorted
@SQ     SN:Scaffold1    LN:540667
@SQ     SN:Scaffold2    LN:419338
• 0 views • link
updated by WouterDeCoster WouterDeCoster • written by ggman ggman

Do the (z) grep on the fastq file. Not the bam file.

• 0 views • link
written by WouterDeCoster WouterDeCoster 
@NB501124:10:H5LKGAFXX:3:21612:11073:20398 1:N:0:
CTTGTNCCTGAGAATGNTGAGCATAACAAGTTTTTTTAACTTGTGTTGTCCCCCATCTCTTTGTGAANCCAANGCAAANCATCCTCAAATAGTAGCCATCGGTAGTCTTTACATC
+
AAAAAEEEEE#EEEEEE

that doesn't look right...

• 0 views • link
written by ggman ggman

As you can see it is missing Q values for a number of bases in that read. If that is the only issue then you could delete that read (and its mate) from R1/R2 files.

• 0 views • link
written by GenoMax GenoMax

thank you for the help geno

could you post it as an answer so I could close this topic?

• 0 views • link
written by ggman ggman

Done. Recopy your result from post above below the answer. Then I can clean this thread up.

• 0 views • link
written by GenoMax GenoMax

1 answer

We would like to see the output of zgrep -A 3 NB501124:10:H5LKGAFXX:3:21612:11073:20398 if your data file is compressed or just grep if it is not.

• 0 views • link
written by GenoMax GenoMax

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