BOWTIE output problems

[jwaage]

Hey all,

In BOWTIE, aligning 75bp reads, setting parameters for only outputting unique reads, works fine (and is damn fast!) - now, I want to output all reads not mapped by using the --unfq paramter. This gives me a FASTQ-file with reads of uneven lengths, skipped lines and general chaos.

Any help is appreciated!

Regards,
JW,
Uni. of Copenhagen

[Cole Trapnell]

Hi JW,

I tried to briefly reproduce this with the latest version of Bowtie, but I couldn't. Could you provide the exact parameters you used to run Bowtie, the version you are using, and perhaps even a small test set that reproduces this issue?

Also, would you please submit this information in a bug report in our tracker:

http://sourceforge.net/tracker/?func=add&group_id=236897&atid=1101606

Thanks for the bug report.

Cole

[jwaage]

Thank you for the quick reply -

FASTQ read file, solexa quality:

>HEADER
NNNNNNNNNNNNNNNNNNNNNNNNNNNNN.......N(n=75)
>+
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...
(Reads per mapping: 2m)

Index: mm9, prebuilt from BOWTIE homepage

BOWTIE Version 0.9.8.1

Command:

./bowtie --solexa-quals -m 1 -p 8 --unfq nm_reads index reads hits

Non-mapped output contains fastq-file with 90% of sequenes correct, but rest has missing lines, sequences longer or shorter than 75bp, merged quality and sequence and so on...

Best regards,
JW

Ps: I can submit a test-set, if necessary

Hi JW,

I tried to briefly reproduce this with the latest version of Bowtie, but I couldn't. Could you provide the exact parameters you used to run Bowtie, the version you are using, and perhaps even a small test set that reproduces this issue?

Also, would you please submit this information in a bug report in our tracker:

http://sourceforge.net/tracker/?func=add&group_id=236897&atid=1101606

Thanks for the bug report.

Cole

[Cole Trapnell]

Hi JW,

This sounds like a synchronization bug. I can't reproduce it with version 0.9.9, and a lot changed between 0.9.8.1 and 0.9.9. Can you download the latest version and try it again?

Thanks,

Cole

[jwaage]

The bug was corrected upon upgrading to the newest version - thank you again for a well documented and solid product!