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Hi,
I am trying to use Prism on WGBS data. After extracting and preprocessing the data, I get the following error at the deconvolution step:
```
prism deconvolute -i preprocess_out/D33_18_LB.…
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I am new to bioinformatics and I am trying to analyze WGBS data using BSseeker2. I am using Python 2.7.13 with Pysam 0.9.1.2. bs_seeker2-align.py terminates after running for 9 minutes indicating an e…
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I'm aligning PE WGBS data using a Bismark wrapper for the bowtie2. Recently, I switched from bowtie2 2.4.2 to the latest 2.5.2 and faced a memory issue.
(P.S: bowtie2 2.4.5 works consumes const mem…
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I installed using pip3. I am trying to run the CpG_aggregation.py test. I downloaded the test files, and am now running `CpG_aggregation.py -b hg19.RefSeq.union.1Kpromoter.bed.gz -i test_03_RRBS.bed …
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Hello,
I was wondering whether BatMeth2 can also directly output the alignments in BAM format? Currently I have to sort the alignments with samtools, but the SAM file is really large and creates prob…
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I have genotype array, WGS, and WGBS data for my samples. I am using this information to detect sample swaps. I find that Biscut genotype calls are highly concordant with WGS genotype calls except for…
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### Operating System
Other Linux (please specify below)
### Other Linux
RedHat 7.9 (Maipo)
### Workflow Version
v2.9.0-gd9e8593
### Workflow Execution
Command line
### EPI2ME Version
_No resp…
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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,
Thank you for developing EpiSCORE. I have been using it to calculate the proportion of cell types making up healthy prostate as well as prostate tumour samples and so have been using mrefPro…
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This should be easy, based on analyzing the nucleotide composition of a collection of reads at the start of the file (e.g. 100k reads).