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There are two errors in the bowtie code.
1 - bowtie = scc + IN_component + OUT_component
This doesn't work, and the code in the book has it correct:
bowtie = **list(scc)** + IN_component + OUT_c…
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I am trying to run PIQ for the 139 Jaspar motif on my dataset. However, I am getting an error during the clustering step.
The previous steps ran without a problem i.e. 'PWM hits across the genome' & …
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I use a totally the same fq, with the same sequence and quality, but only the read name differ. And got a different algnment result, here is one example of a read:
![de463d9bc779358fdb68182b5f1a147](…
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A `bowtie suite` or `bowtie run` execution treats test failures by still exiting with 0 exit code, as failures are part of Bowtie's "normal behavior" as a compliance checker.
However -- *errors*, p…
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Hello.
I know `emirge` has only been tested on versions 0.12* or so of `bowtie`. But, we had no issues running it up to version 1.1.2 of `bowtie`. A recent upgrade to `bowtie 1.2`, however, broke `…
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One of the important contributors to the JSON Schema (@Julian) has released what is called a meta validator of JSON Schemas. It can be used to test our schema across multiple JSON Schema implementatio…
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Hi,
there is another [bug report](https://bugs.debian.org/887578) concerning bowtie tests. The error message in the build is:
# Failed test 'bowtie success'
# at t/Bowtie.t line 188.…
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Hi,
When I ran HiC-pro, I found the result of allValidPairs is 0 kb. The log file shows that in mapping_combine.log, an error: [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0002…
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Hello,
If the reduced genome is composed only of unique RE adjacent sequences, how is it possible that when I run bowtie 2 using the command that is provided in your manual, I get sequences that a…
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Thank you for the software.
TEsmall uses bowtie1 with the specific parameters to map and filter the reads. Is there any specific reason to use bowtie over the the bowtie2/star with the similar param…