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Hi,
I am checking MHL values of my BAM files and see something unexpected. The sample BAM I can share holds alignments of amplicon bisulfite sequencing of five regions to a very high depth (5000-5000…
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Hi there,
since GDC release 23 there is a new readout for TCGA, 'Allele-specific Copy Number Segment'. It would be great if it were downloadable in TCGAbiolinks via:
```R
query.cnv = TCGAbiolin…
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Hello
I am working with human whole-genome bisulfite sequencing data, and paired-end reads. After using Trim Galore to remove adapters, I encountered an issue with the FastQC report for R2 reads ac…
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**A reproducible template workflow for single-cell DNA methylation data**
DNA methylation is a heritable epigenetic mark that shows a strong correlation with transcriptional activity, and may be de…
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Hello,
Is adapter trimming required or recommended for WGBS analysis using gemBS?
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Dear yupenghe,
I would like to know whether methylpy can be used for methylation analysis of plant genome because the results I get using methylpy are quite different from those of Bismark.
Thanks.
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http://doi.org/10.1038/srep19598
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Thinking about DNA quantity, targets, and cost I would like to develop a Diagram that outlines meth-seq options.
Given @yaaminiv is in thick of this, could you please start this. Things we should con…
sr320 updated
5 years ago
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A "as simple as possible" init script usable for each DEEP pipeline that identifies itself (WGBS, ChIP-seq etc.) and loads - if necessary - required reference data/configurations from the reference re…
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Hello,
**I ran Bis-SNP1.0.0 from he prompt line using the following command:
(Java version: JDK8)**
java -Xmx10g -jar BisSNP-1.0.0.jar \
-R mm10.fa \
-I file.bam \
-T BisulfiteCountCovariates …