User: MMa
MMa • 280
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Posts by MMa
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... I'll be a bit more technical here.
`bdgdiff` first generate three tracks from the 4 input tracks, which contains the log-likelihoods of t1 > t2, t1=t2, and t1 < t2. The three output files are in fact peaks called by `bdgpeakcall`--the subfunction for calling narrow peaks--from these three tra ...
written 8 months ago by
MMa • 280
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... Hi,
We have a large set of tumor-only WES data that we want to run `music smg`. However, it's unclear from the documentations on whether:
1. Matched tumor-normal bam files are required for `music smg` *per se*,
1. Running `music bmr calc-bmr` is necessary before running `music smg`, and
1. I can u ...
written 15 months ago by
MMa • 280
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... I know that many transcripts having frameshift mutations will be degraded by nonsense- or readthrough-mediated degradation, subject to rules that are well-known.
How how about start-loss? Most likely they won't be translated if they don't have an alternate start codon, but will they be degraded qui ...
written 22 months ago by
MMa • 280
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... Well, the somatic callers I used (MuTect, MuTect2, VarScan, MuSE) do not call somatic reversions, which I hope they could.
That aside, using only default parameters and nothing else on a particular pair I'm currently working, MuTect gives less than 2,000 variants and MuSE gives less than 500. I'd b ...
written 22 months ago by
MMa • 280
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... I understand this. The purpose of the variant calling in question, however, is not to study their biological significance. I plan to do some RNA-editing research, so I need to identify DNA-level variations to act blacklist positions. ...
written 22 months ago by
MMa • 280
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... Hi @igor, the intention is to identify all variants regardless of source. ...
written 22 months ago by
MMa • 280
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6 follow
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... Hi all,
I am looking to identify DNA-level variations from a matched tumor-normal WES data. Specifically, I just want to know the variations in the tumor sample in relate to the *reference genome*, not the normal sample.
I have noticed two possible approaches here:
1. Simply use a germline-varia ...
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... Eventually I got to try out this one. The important `GenomicFeatures` function here is `mapToTranscripts`:
library(GenomicFeatures)
library(rtracklayer)
gencodeTxDb <- makeTxDbFromGFF (file="gencode.annotation.gtf")
gencodeTx <- transcripts (gencodeTxDb)
names (gencodeTx) ...
written 23 months ago by
MMa • 280
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... I know this is an old thread, but SSGSEA can be calculated using the Bioconductor package GSVA. If you use RPKM, use `ssgsea <- gsva (RPKM, method="ssgsea", kcdf="Gaussian", ...)`; if you use raw counts, use `ssgsea <- gsva (counts, method="ssgsea", kcdf="Poisson", ...)` ...
written 23 months ago by
MMa • 280
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... The docs for the current versions of pindel states depth is the same I'd get from `samtools depth`. ...
written 2.3 years ago by
MMa • 280
Latest awards to MMa
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Adding Coverage Stats into MuTect2 output VCFs
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Is log-transformation needed to calculate Euclidean distance metric from FPKM/TPM?
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Mapping between genomic coordinates to transcriptomic coordinates
Student
22 months ago,
asked a question with at least 3 up-votes.
For Adding Coverage Stats into MuTect2 output VCFs
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: Different results with edgeR when adding gene symbols
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: Different results with edgeR when adding gene symbols
Scholar
2.4 years ago,
created an answer that has been accepted.
For C: I get the same modules but different number of genes WGCNA
Scholar
2.5 years ago,
created an answer that has been accepted.
For C: I get the same modules but different number of genes WGCNA
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