User: MMa
MMa • 240
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Posts by MMa
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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 6 weeks ago by
MMa • 240
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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 8 months ago by
MMa • 240
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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 8 months ago by
MMa • 240
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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 8 months ago by
MMa • 240
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... Hi @igor, the intention is to identify all variants regardless of source. ...
written 8 months ago by
MMa • 240
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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 8 months ago by
MMa • 240
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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 9 months ago by
MMa • 240
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... The docs for the current versions of pindel states depth is the same I'd get from `samtools depth`. ...
written 13 months ago by
MMa • 240
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... I got from our collaborator some pindel output and the BAM files that is used as pindel input. Unfortunately, they used an older of version of pindel (before approximately 0.2.4u) that doesn't record total depth at breakpoint (i.e. the DP field in VCF). While our collaborator's standard practice is ...
written 13 months ago by
MMa • 240
• updated
12 months ago by
Pierre Lindenbaum ♦ 111k
Latest awards to MMa
Student
8 months ago,
asked a question with at least 3 up-votes.
For Adding Coverage Stats into MuTect2 output VCFs
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Different results with edgeR when adding gene symbols
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Different results with edgeR when adding gene symbols
Scholar
15 months ago,
created an answer that has been accepted.
For C: I get the same modules but different number of genes WGCNA
Scholar
15 months 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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