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Hi Tobias:
In my experiment(1mM 4sU pulse for 30 min), before library construction, all the steps followed the standard protocol of SLAMseq, after total RNA extraction the rRNAs were removed from t…
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Hi Tobias,
Could you kindly help me with the following 2 questions?
1. The slam-seq library was prepared with Lexogen kits and should used single-end sequencing. But the sequencing center returned…
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Hi, @t-neumann. Thanks for the amazing technology.
We are currently processing some slam-seq data. We are running our fork of Slamdunk, [https://github.com/jkobject/slamdunk](https://github.com/jko…
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Hello,
Thanks for the nf-core slamseq package. I have it run well using `slamdunk all`, this run from raw reads to count files. I'd like to have DEG analysis as well, so I tried this on the nextflo…
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Hi I am trying to run HLEB to estimate half life time with chase time points 0h, 1h, 5h, and 12h. I noticed that in the Molecular Cell paper [https://www.cell.com/molecular-cell/fulltext/S1097-2765(23…
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Hi there, if i wanna use 4sU pulsed total RNA to construct strand-specific library followed by the SLAM-seq protocol with the exception of library construction step, in this context, rRNA will be remo…
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Dear Team,
I am new to SLAMseq and trying to use SLAMDUNK for the analysis of my Slamseq data. When I am running the command "alleyoop utrrates -o try/ -r /ref/genome.fa -mq 27 -m -t 64 -b /ref/ge…
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Dear Neumann:
I tried to repeat Figure 3 and calculate the CPM value of T>C, which is about 100 times larger than the figure in the paper. I use R script for tcount.tsv, the calculation formula is …
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Hi there; as a preface, I am very new to bioinformatics, but I have had some issues in running the slamdunk count / alleyoop utrrate commands. When I put the following into my terminal, all that happe…
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Hi t-neumann,
Thanks for creating this awesome tool.
I was trying to run alleyoop after `slamdunk all`.
command:
```
# How I run slamdunk all
REF_FA=/tscc/nfs/home/hsher/gencode_coords/G…