Unable to create star refernce file with rsem
0
1
Entering edit mode
5.3 years ago
Debbie ▴ 10

Hi all,

I am trying to analyze my RNA-seq data with RSEM by using STAR aligner.

For this I downloaded the gtf file, hg19 genome and is using the following code

rsem-prepare-reference --gtf hg19-iGenomes.gtf --star /data/RSEM/hg19 hg19_rsem

based on RSEM usage "rsem-prepare-reference [options] reference_fasta_file(s) reference_name"

where "/data/RSEM/hg19" contains the .fa file (fasta files) for all the chromosomes and hg_rsem is the reference name or --outFileNamePrefix.

It is generating the output files hg19_rsem.n2g.idx.fa, .idx.fa, .seq, .transcript.fa, .chrlist, grp, ti and chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt, hg19_rsemLog.out, hg19_rsem_STARtmp.

However, it is ending with:

Aug 22 13:34:46 ..... started STAR run

Aug 22 13:34:46 ... starting to generate Genome files

Aug 22 13:35:57 ... starting to sort Suffix Array. This may take a long time...

Aug 22 13:36:22 ... sorting Suffix Array chunks and saving them to disk...

"STAR --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeFastaFiles /data//RSEM/hg19/chr1.fa, ........ /data/RSEM/hg19/chrY.fa --sjdbGTFfile hg19-iGenomes.gtf --sjdbOverhang 100 --outFileNamePrefix hg19_rsem" failed! Plase check if you provide correct parameters/options for the pipeline!

I am unable to understand where I am going wrong. Please help me sort this out.

Thanks Debbie

RNA-Seq rsem-prepare-reference • 2.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 2675 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6