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Complete cost analysis for different methods (RRBS, WGBS, and Amplicon-based BS-seq) and include it here:
https://docs.google.com/presentation/d/1mD6ivb3xcfhvu_fF7dhYTLWytzXeYp8rheEvbTJKWnc/edit#sl…
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Hi Felix,
By using the amazing Bismark, we can get the methylation percentage of a specific position. And we also can get the number total methylated C from *_report.txt file.
I am cu…
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Hi,
I was using plot roc function to plot AUC:
(tombo_36) [wangj@helix tombo]$ tombo plot roc --statistics-filenames mathylation_testing.5mC.tombo.stats --genome-fasta $genome_fasta
***…
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FIU folks would like specific advice on MBD-BS library prep and sequencing
I am thinking what was done for Yaamini's Cv samples.
I imagine there is not a url that captures it all..
What kits were…
sr320 updated
5 years ago
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Hello,
I am trying to create a gemBS index for GRCh38, specifically this fasta: https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/ . However, it always fails at exactl…
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Here is at start
https://github.com/RobertsLab/code/blob/master/20-bismark.sh
sr320 updated
5 years ago
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Dear Felix,
I have a few question about bismark and bismark methylation output.
1. after some bismark optimization using `-I 0 -X 1000` and `--score_min L,0,-0.4` I got a better mapping efficien…
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Hi,
The alignment task is taken to a failed state if there are no ALT contigs (`ref_alt` file has no content). Why is this?
In the command `ref_alt` is not used but there's an if statement requi…
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Hi Felix,
I have a problem about the ambiguous reads. I want to get all of multiple alignment positions.
But I use the options --ambig_bam to run Bismark ,but it only can output one of multiple al…
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https://github.com/BIMSBbioinfo/pigx_chipseq/blob/407ac9b8ef4e69e6c7483eea57f2bfb6103c7a4e/scripts/Functions_Helper.R#L123