User: pel

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pel10
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2 years, 10 months ago
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Posts by pel

<prev • 11 results • page 1 of 2 • next >
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Comment: A: Where is the pathogenicity in TCGA MAF files?
... Thanks - very helpful. Lately we have been fetching TCGA data from cBioPortal at your institution, so a couple of questions (thanks in advance). -It seems that the Provisional "_tcga" data sets seem to be widely used, and the other datasets for the same cancer subtypes appear to be datasets that ...
written 3.0 years ago by pel10
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Fetching mrna values from cBio-Portal Web API
... Using .NET and HttpResponse I can successfully fetch mutations and copy number alterations successfully for a gene list using the web-API url below; however, when using "mrna" there is a "can't find study error" url = "http://www.cbioportal.org/webservice.do?cmd=getProfileData&case_set_id=" &am ...
rna-seq written 3.0 years ago by pel10 • updated 3.0 years ago by Biostar ♦♦ 20
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GISTIC 2.0 run of COSMIC CNA data?
... Is it possible to somehow feed the CNA data from COSMIC format into e.g. GISTIC 2.0 to obtain, for each gene, one of the 5 possible copy-number levels: -2 deep loss, -1 shallow loss, 0 diploid, 1 low-level gain, and 2 high-level amplification? I have also heard of an algorithm called RAE, but don't ...
cna cosmic written 3.0 years ago by pel10 • updated 3.0 years ago by Biostar ♦♦ 20
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Answer: A: TCGA data set with both expression (rna seq/ microarray) and exome seq of same
... You can find the largest selection of level2 and level3 (no human subjects protocol required) data for somatic mutations, CNVs, SNPs, methylation, and RNA-Seq and chip-based expression for each tumor in TCGA for multiple cancer sites at the [PanCancer 12 site][1] Recall, as was pointed out above, ...
written 3.1 years ago by pel10
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Where is the pathogenicity in TCGA MAF files?
... There does not appear to be pathogenicity prediction results in most of the MAF files from TCGA. Should one only use nonsense mutations? ...
tcga somatic mutations pathogenicity written 3.1 years ago by pel10
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Synapse (Pancancer) archive of MAF somatic mutation files and RNA-Seq expression files
... We are search of an archive which provides the majority of level 2 MAF putative(confirmed) somatic mutations as well as RNA-seq based transcription levels for the majority of cancers(leukemias). Given this, is Synapse (pancancer) currently the most comprehensive archive for collections of various ...
tcga rna-seq mutations cancer written 3.1 years ago by pel10
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Comment: C: Rat lung transcriptome
... thx - used the table browser at UCSC, downloaded the fasta mRNA sequences for the rat transcriptome, then created an index using bowtie_build. ...
written 3.8 years ago by pel10
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Rat lung transcriptome
... We ran RNA-seq for rat lung tissue, and need to build an index for tophat2 (bowtie) that reads this index (fasta).   I searched for downloads of rat transcriptomes at UCSC and noticed most of their data is genomic.   Has anyone produced a rat lung transcriptome fasta?   ...
lung rat rna-seq transcriptome written 3.8 years ago by pel10
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Comment: C: Bowtie alignment with two reads per sample
... ok, thx for the info! ...
written 3.8 years ago by pel10
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Comment: C: Bowtie alignment with two reads per sample
... Thanks for the syntax for coupling the read files.   We have to align to the rat, and I am not sure if the UCSC genome references in bowtie are for the transcriptome(?)  I believe you are correct, since the lab director said the data were from mRNAs, and I am not sure how bowtie2(bowtie) delineates ...
written 3.8 years ago by pel10

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