Daniel Malzl

[BUG] conda recipe is outdated and leads to 'check_pickle" kwarg error with joblib

4

**Describe the bug** I recently used pomegranate to train HMMs on some data. I installed it via conda and assumed I had the newest version. However, after trying to train...

some samples fail with --force_sratools_download due to changes in prefetch results

12

### Description of the bug It is now over a month that I handle my data with `fetchngs` and I am pretty satisfied with the results. However, I recently encountered...

Choice between fastq and fasterq-dump when using --force_sratools_download

2

### Description of feature Hi it's me again, After solving all the issues related to my ncbi config file I stumbled yet across another pitfall connected to parallel file system...

Wrong use of --progress in prefetch command leads to failure of pipeline

16

### Description of the bug I am currently trying to retrieve 15k samples from SRA. Since FTP download was painfully slow due to an apparent connection limit I defaulted to...

max chrom size too small

8

Hi there, I am using pairix in conjunction with cooler to generate cool files for my Hi-C data. Pairix generation seemed to work without an issue using `cooler csort pairix`....

SRAtools download seems to insert paired-end suffix into workdir path

7

### Description of the bug I am downloading data from SRA using the SRA-tools suite. Prefetch finished without an issue. However, fasterq-dump failed with the following error: From the looks...

Taiji fails during RNA-seq read of quant data

2

Hi, I am currently trying to run Taiji on a set of WT and KO RNAseq and ATACseq data. To not mess with previous analyses I decided to use the...

just a view suggestions

5

Hi, After doing Hi-C stuff for a year now I think I finally got some grip on how to do things and since I am a Python person I very...

When calculating the directionality index using the `cooltools.directionality.directionality` function the `balance` argument is not passed on to the `dirscore` function it uses. This results in a KeyError when the `'balanced'`...

When installing the pipeline it starts with downloading and preparing the used ontologies. This process fetches the newest versions of them which work perfectly fine. However, when running the pipeline...