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Hi
fragCounter using CBS algorithm calculate read couts ratio between tumor and normal sample in 200bp genomic bins.
I would like to ask which is the output parameter of the normal sample? Thi…
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Hi Youngbin and Dominik,
Really neat approach! We're interested in trying out SCINPAS on some public scRNA-seq datasets to detect expression of a pre-defined list of target PAS. We've processed our…
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If this folder is really useful, then we should explain why and how. But is it ?
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I think I still encounter an issue that is similar to issue#32
i.e., I did not get the psites_number table in the hdf5 file.
```
group name otype dclass dim
0 / p_si…
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### Description of the bug
I am using Sarek with a configuration that reads UMIs from the FASTQ read names.
The workflow fails at the "MarkDuplicates" step with the error message:
```htsjdk.samto…
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Hello Whippet team!
I am trying to build a BAM supplemented index on Whippet. I used samtools to combine multiple bam files, remove duplicates, sort and index the bam file. Since the chromosomes ar…
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Many pipelines (including ours at NHGRI) are shifting towards doing everything with BAM files. We get output from the sequencing center in BAM format. Ideally, we would like to not have to convert to …
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We have a [HiC-related tool](https://github.com/maxplanck-ie/HiCExplorer) that's [available in Galaxy](https://toolshed.g2.bx.psu.edu/repository/browse_repositories?sort=name&operation=view_or_manage_…
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I'm not clear about which version of mttonucratiocalculator that EAGER-CLI 1.92.55 expects, since EAGER it seems to pass it 3 arguments, whereas mttonucratiocalculator only expects two.
```
$ mtto…
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Getting an error at the database build step:
Adding reads.
Traceback (most recent call last):
File "/home/ok321/anaconda3/bin/rpe", line 8, in
sys.exit(main())
File "/home/ok321/anacon…