More posts like this
-
Understanding TCGA's ASCAT copy number data
written by loughrae 9Hi all, I'm trying to understand TCGA's Level 3 copy number data. Specifically, I found two tables that appear to be made via ASCAT, and …
-
Getting sample IDs from dbGaP SRR?
written by vctrm67 9Does anyone know how to get the actual sample IDs from downloaded and extracted SRA files? Right now they are in the form "SRR..._dbGaP" but …
-
Interpreting GISTIC2 output
written by vctrm67 9I am wondering how to get GISTIC to output, or how to post-process, data that shows **copy number change per gene relative to a threshold …
-
Amplification over deletion/Deletion over amplification?
written by vctrm67 9I am running GISTIC on some modified ASCAT copy number profiles. Part of the algorithm is a deconstruction/reconstruction of the copy number profile to find …
-
GISTIC 2.0 for sequencing data
written by vctrm67 9I am looking to hopefully run GISTIC 2.0 on some CNV calls I have from sequencing data. However, the input file requires the following fields: …
-
ASCAT CN vs SNP probes
written by vctrm67 9Does anyone know the difference of these and how these are used in ASCAT? To my understanding, ASCAT uses SNP probes to determine SNP status …
-
TCGA CNV data reformatting
written by vctrm67 9I have TCGA data that needs to be reformatted according to the following: # 'x' is a matrix of segmented output from ASCAT, with at …
-
How to analyse number of breakpoints -TCGA data
written by berry 4Hi, I have TCGA segment files and I want to analyse the number of breakpoints. Does anyone know how to calculate it? Thanks!
-
Picard CollectWgsMetrics for each chromosome? Standard deviation of coverage per chromosome
written by QVINTVS_FABIVS_MAXIMVS 259Hi I'm running Picard on some BAM files and noticed that the default output for CollectWgsMetrics is for the whole genome. I would like to …
-
TCGA data, Num_Probes and Segment_Mean
written by joshwarrick 1I'm starting to use TCGA data. Level 3 data SNP data determining CNV have the following format: ``` Sample Chromosome Start End Num_Probes Segment_Mean BEDEW_p_TCGA_FFPE_7_13_N_GenomeWideSNP_6_A05_1347396 …
I think this info can be extracted in SAMPLENAME.tumor.LogR.txt file or, in less convenient manner, in SAMPLENAME.LogR.PCFed.txt