Incorrect results when using large index about bowtie HOT 14 CLOSED

We are finally looking at this and can confirm that we've recreated it. We also see it for unpaired reads. We're investigating.

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I would like to recreate this issue. It will be helpful to have the fasta file and the command line used for generating the small indexes as well.

from bowtie.

Okay, this dropbox link is the complete fastafile, which I used for the large index (I will disable this link later on).

The file was split in two using this command: split -l 161150 -a 1 -d cdna_unspliced.fa splitfile_part

And the bowtie indexes were all generated with the simplest version of the bowtie-build command:
For the large index:

bowtie-build cdna_unspliced.fa large_index

And for the small indexes:

bowtie-build splitfile_part0 small_index_part1
bowtie-build splitfile_part1 small_index_part2

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@ch4rr0 Did you manage to recreate the issue?

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Hello @mluypaert,
My apologies for the delayed response.

Yes I was able to recreate the problem. Unfortunately the work required to have this resolved is nontrivial, so we will delay this fix until the next bowtie release. We currently don't have a timeline for when this release will be, but I will keep you posted as soon as it's decided.

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Hello @ch4rr0

I see on the bowtie website that version 1.2.0 was released on 12/12/2016. However I don't see anything in the changelog about the large-index bugfixing (this issue). I assume this was not fixed in release 1.2.0 yet? Any idea on what release would contain this fix and when to expect it to go public?

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@ch4rr0 @BenLangmead Can you please give me an update on this issue? Are there any timelines on when we could expect this issue to be fixed (by when and in what release)?

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I am sorry for letting this one slip through the cracks. I have started looking into the issue and will reply to this thread as I progress.

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@ch4rr0 Any progress updates yet?

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Hello, I have yet to find the underlying cause of this problem, but still continue to investigate.

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Would it be possible to re-upload the reference file to dropbox?

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I believe this was the input fasta used to build the large index: https://www.dropbox.com/s/obuwxzmc309e66f/cdna_unspliced.fa?dl=0
This link will expire in 30 days.

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Thank you. I have saved the file locally.

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A fix for this issue was included as part of our most recent release.

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