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Hi Ian and Tom,
Hope you are well.
We are running a splice junction analysis using human plasma samples processed on a Novaseq 6000 ( RNA sequencing with UMIs).
Analysis Pipeline in brief :
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SJJHK updated
6 months ago
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I have RNA modbams with m6A (in DRACH motifs) and everything runs without error but wgmeth/differential methylation results are sort of confusing - are there going to be RNA-specific additions to meth…
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Hi,
I am getting following error when selected gmap only with sample data provided with pasapipeline as well as my own data as well. I used updated version of gmap.
-connecting to MySQL db: rice_p…
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I'm currently trying to run `hisat_genotype` in a `docker` container due to #66
Below is my `Dockerfile`
```
FROM biocontainers/biocontainers:vdebian-buster-backports_cv1
USER root
ENV DE…
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Hello, I am interested in the application of this tool to 10X multiome data. I have the following output files from CellRanger:
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi
filtered_feature_bc_m…
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I helped a colleague debug an issue with nanopolish call-methylation, whereby a BAM file with no spliced alignments would be detected as having a spliced alignments, leading to the program stopping. T…
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I have the full Augustus annotations of a closely relates strain that had been trained through Braker using RNA-seq. Is it possible for me to use the output of that annotation as input for Augustus to…
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When I run **BAMboozle 0.5.0** on BAM files generated with **Salmon 1.6.0**, I get the following error message:
```
BAMboozle --bam sample01.bam --out sample01.anonym.bam --fa /mnt/data/reference_…
matmu updated
11 months ago
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Hi Ben and Kasper,
Now we are conducting a project utilizing data from GTEx project. We are particularly interested in the resource presented in recount3 and would like to seek clarification on two…
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Hello, I've been using ONT's full-length transcript data for genome annotation recently, but it seems that minimap2 doesn't handle some complex regions very well. I had a great experience using winowm…