TCGA data aligner

[Irina Pulyakhina]

Hi everyone,

Does anyone know what aligner was used for the TCGA data (could not find this info on the amazingly "handy" website, feels like they are trying to hide it)? I am interested in the aligner used for whole exome sequencing and mRNA sequencing data from breast cancer.

Regards,
Irina

[Irina Pulyakhina]

Found it:

reference for WXS:
-> http://www.biomedcentral.com/1471-2105/15/247 (in the Methods section)

reference for RNA-Seq:
-> https://tcga-data.nci.nih.gov/tcgafi...ESCRIPTION.txt

So BWA was used for the alignment of both whole exome sequencing and RNA sequencing data

-Irina

[GenoMax]

TCGA mRNA-seq pipeline: https://webshare.bioinf.unc.edu/publ...eq_summary.pdf

[Irina Pulyakhina]

Thanks GenoMax! But this is weird -- your link says they used MapSplice for RNAseq alignment, and this one says they used BWA for RNAseq alignment:

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/read/cgcc/unc.edu/illuminaga_rnaseq/rnaseq/unc.edu_READ.IlluminaGA_RNASeq.mage-tab.1.3.0/DESCRIPTION.txt

So which one should we trust?..

-Irina

[GenoMax]

There is probably two sets of data are two different pipelines. Document from NCI (from 2011) was for v1 data.

Second document (from 2013) refers to level 3 data for the ‘rnaseqv2’. What dataset are you looking at?

[Irina Pulyakhina]

I am looking at level 2 data (I am doing my analysis on the bam files directly), but I would think that bam files generated at level 2 would be used for all the calculations at level 3, wouldn't this make sense?

[GenoMax]

Here is an update from TCGA.

The V1 analysis (old) used BWA and the V2 analysis (new) uses MapSplice.

@Irina: The Description file you had linked from NCI site was from a V1 directory. Everything that was V1 has been reprocessed as V2. There should be a description file in every mage-tab folder at DCC.

See this link for current supported version with details about the V1 and V2 pipelines:

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/read/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_READ.IlluminaHiSeq_RNASeqV2.mage-tab.1.9.0/DESCRIPTION.txt

From the description file
V1_BWAtoTranscriptome, V1_RNASeqQuantification: UNC V1 RNA-Seq Workflow - BWA Alignment to Transcriptome

Date: 20101108

V2_MapSpliceRSEM: UNC V2 RNA-Seq Workflow - MapSplice genome alignment and RSEM estimation of GAF 2.1

Date: 05-10-2012

The SDRF and IDF files link the bam files with the aligner used.

[Irina Pulyakhina]

Everything is clear now, thanks!