[GenoMax]

Files referred to in the last post by @Sajna are once again available at the same link.

[Sajna]

As per the RNASeq version 2 pipeline in the link below, I have been able to obtain outputs till step 11, i.e the transcriptome_alignments_filtered.bam output. Next step is to run rsem.

https://cghub.ucsc.edu/docs/tcga/UNC_mRNAseq_summary.pdf

I ran RSEM using the following command : /opt/rsem-1.1.13/rsem-calculate-expression --paired-end --bam --estimate-rspd -p 8 transcriptome_alignments_filtered.bam /home/group_sh/TCGA+SRA_datamergerquantification_RNASeqV2/RSEM_ref_from_TCGA_webshare/hg19_M_rCRS_ref ERR519523.rsem > rsem.log_2 > rsem.log

I get this error in the log file :

rsem-parse-alignments failed! Please check if you provide correct parameters/options for the pipeline!

What is wrong? I donot understand. I am running exactly the same command!!!

Kindly help.

[GenoMax]

Are you using a different version of RSEM than the one in the PDF?

[Sajna]

No. I am using the same version mentioned in the UNC mRNASeq version2 document.

[GenoMax]

Have you done first part of step 4 in this document: https://tcga-data.nci.nih.gov/tcgafi...ESCRIPTION.txt

[Sajna]

Yes, I have done the first part of step 4 from that doc. I have the transcripts_aligned.bam, furthur filtering is also done. The only thing thats not working is RSEM...which we need!!!

[GenoMax]

Write directly to the contacts included in the TCGA doc with a request for help.

[Sajna]

Ok. I will do that. Will update on the same once I receive the reply. Thanks.