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Hello,
I am trying to use the cnv_ltffinder2gff.pl and I keep getting this error:
```
stephenwyka@bspmgenomics:/data/wyka/transposable_elements/LM470$ ../../dawgpaws/scripts/cnv_ltrfinder2gff.p…
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Hello,
First thank you for your work. I would like to test your tool on other sub-families of transposable elements so I'm trying to follow the instructions but I have some questions.
I have a …
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When I run RetroSeq in the align mode, it gets to PE alignment parsing and then breaks. Not sure what the error means (uninitialized value before assignment?).
Input: perl bin/retroseq.pl -discover -…
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Hello,
I ran the test data in the login node of HPC cluster:
```
nextflow run /public/home/zyqi/pan-TE-analysis/GraffiTE/GraffiTE/main.nf \
--assemblies assemblies.csv \
--TE_library huma…
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Hi Alex,
I have a question about best practices for dealing with multi-mapping reads in scRNA-seq data analysis, particularly when looking at transposable elements (TEs). Due to the nature of TEs,…
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Hi,
I just got the count matrix from TElocal.
I would like to compute the TPM to perform within-sample comparison but the matrix is a mix of genes (I got ensembl ID, from annotation provided wit…
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For now the pipeline uses the gencode bedfile to measure chromatin accessibility around the gene body.
We want to include other bedfiles, such as protein binding sites or repeat.
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- [x] discuss shortly the pipeline and its configuration with MS
- [x] check fastp documentation bc paired end (PE) needs additional sequence_r parameter here https://github.com/epigen/atacseq_…
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Hello,
Thanks for scTE!
I did run it in my mouse scRNA seq data, however, I haven't been able to read the output file... it is too big!
I have a .csv of 60gb for each of my samples and I can't read…
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Dear @oushujun ,
Thank you for developing this useful tool. I have run it successfully and found that SINEs and LINEs could't be identified based on structure features. However, we didn't have such T…