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Add a rule to tofu.partition.snake to extract flnc reads that don't map anywhere with QV40.
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Dear Authors
I am trying to map some genomic reads (nor transcriptome or RNA-seq) with medium to long size length (above 1-15 Kb). Is HISAT2 an appropriate tool to align these reads onto a referen…
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Hi there,
I'd be interested in mapping noisy long-reads to assembly graphs (in GFA format), to untangle paths through repetitive parts of the graphs.
Here is another github issue (https://github…
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#### Describe the bug
Sample NIRS data in the BIDS format can not be read due to some problems with channel names. This applies to the data set in the example below, but can be replicated with the da…
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When doing all-vs-all do not look for anchors of reads with the same `read_id`. Currently we are doing this for the sake of code simplicity, but this introduces additional overlaps which probably affe…
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### Feature type
Changing existing functionality
### Improvement Description
The mapping of model variables to external names (e.g. in the TOM config file and BMI) is one to one. For example, the `…
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Hello! We were looking at the exon counts again and saw some discrepancies from what we expected. This one comes from reads going on one strand counting as being excluded from the gene on the opposite…
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### Before reporting an issue
- [X] I have read and understood the above terms for submitting issues, and I understand that my issue may be closed without action if I do not follow them.
### Area
a…
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Hello
Thank you for your convenient reed2tree tool and I am very sorry to cause you trouble again.
When I followed the coronavirus dataset analysis [tutorial](https://github.com/dvdylus/read2tre…
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Hello,
I'm getting the following error as shown below when running on a series of bam files. Bam files we're generated by mapping to a consensus sequence generated from an initial alignment
`T…