User: MMa

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MMa280
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Posts by MMa

<prev • 37 results • page 1 of 4 • next >
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Answer: A: Narrow & Broad peaks from 'macs2 bdgdiff'
... 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 MMa280
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Does a no-normal pipeline exist for MuSiC?
... 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 ...
music written 15 months ago by MMa280
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How likely do cDNAs with start-loss variants appear in mRNA-seq?
... 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 ...
rna-seq written 22 months ago by MMa280
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Comment: C: Strategies to call variants from a cancer sample
... 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 MMa280
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Comment: C: Strategies to call variants from a cancer sample
... 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 MMa280
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Comment: C: Strategies to call variants from a cancer sample
... Hi @igor, the intention is to identify all variants regardless of source. ...
written 22 months ago by MMa280
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Strategies to call variants from a cancer sample
... 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 ...
next-gen snp written 22 months ago by MMa280 • updated 22 months ago by d-cameron2.1k
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Comment: C: Mapping between genomic coordinates to transcriptomic coordinates
... 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 MMa280
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Answer: A: ssGSEA on RNA-Seq data from TCGA
... 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 MMa280
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Comment: C: How to get sequencing depths from VCF with Rsamtools
... 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 MMa280

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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