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For Differential Expression analysis do you use TcReadCount/ReadCount or ConversionsOnTs/CoverageOnTs as input? What will be the difference in outputs for fold change for these two inputs?
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Hi Tobias,
I was trying to run the slamdunk docker image using Singularity. In the past, I have been successful running both slamdunk and the alleyoop commands this way. But recently the utrrate h…
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Now that we finally got to see `nf-core sync --all` [run for real with all repos](https://github.com/nf-core/tools/runs/458082607?check_suite_focus=true), we can see a few improvements that would be g…
ewels updated
4 years ago
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For our experiments, we used Lexogen catabolic Slamseq kit and we were able to analyze our data by using your Slamdunk software. It's clear that T>C conversion was dramatically higher than other base …
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Hi Tobias,
I have looked through the issues and a few people have asked about background levels, but for very specific cases. I'd like to ask more generally, what kind of background TC counts do yo…
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Hi Tobias,
I was able to avoid the issues with #65 by using the Docker image you have on Docker Hub. Thank you for providing that. However, I have encountered a new error. The stdout looks like:
…
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Hi again t-neumann,
Thanks for answering my previous questions. I am trying to rerun slamdunk all with the -mts flag; however, I keep running into this error:
```
`usage: slamdunk all [-h] -r R…
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Please help:
-mbp:Slam-seq xbing88$ slamdunk filter -o output -b mm10_miRNA.bed S13_bowtie2_sorted.bam
Running slamDunk filter for 1 files (1 threads)
[W::hts_idx_load2] The index file is older t…
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I am trying to run slamdunk all using UCSC 38 genome and corresponding 3utr.bed file with my samples formatted as specified in a text named sampleInfo.tsv as shown:
`$ slamdunk all -r genome.fa -b 3…
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Hi Tobias,
I want to install slamdunk on the cluster (Linux 3.10.0-862.14.4.el6.x86_64) where I only have the write permission to my user home directory.
I chose to use Anaconda2 to install slam…