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I am using deeptools bamCoverage to analyze short (35-80bp) paired end fragments. All reads in my bam file are properly paired based on samtools flagstat and Picard. Yet bamCoverage extends some a…
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Hi, I have read paper of SViCT and tried to use this tool for my analysis.
The compilation was successful and ran this tool using cfDNA sample and the core dump has raised.
Command line I have u…
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I have just started exploring use of DMRcate for DMR detection but have concerns about the approaches dmrcate offers for ranking DMRs. DMRcate offers Fisher's combination, Stouffer's combination, and …
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I have observed cases where my dual UMIs can get swapped during amplification steps in library prep, resulting in two consensus sequences which align to the same start/stop position but share the half…
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reported by [a user](https://groups.google.com/g/cbioportal/c/WQcWgsHz1e4/m/c-TfVDQVCwAJ)
In [this patient](https://www.cbioportal.org/patient/summary?sampleId=CD08&studyId=ucec_ccr_cfdna_msk_2022)…
jjgao updated
3 months ago
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**Describe the bug**
After recompiling the binaries from source for AVX-512 cores Octopus no longer runs as normal, producing error:
'Phred: negative error
[2024-07-15 12:55:12] probability -…
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https://mp.weixin.qq.com/s/3b3j68dXLHZSHzCc1uVYJA
ixxmu updated
2 weeks ago
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How to prepare data for WGBS data , Thank you!
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Is the tagged BAM output already corrected (i.e. adds/subtracts reads to account for GC bias based on correction weight matrix created)? Or does this need to be done after the fact?
Thanks!
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Hi, thanks a lot for this tool!
I'm having some problems I cannot identify, please:
This is my code...
```
$ bedtools genomecov -bg -ibam 160023_IGO_15698_6.v2.sorted.markdups.bam > tmp.bedg…