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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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rsem-parse-alignments problem #112

Closed lybird300 closed 5 years ago

lybird300 commented 5 years ago

Hi there,

I'm having the same problem as the already closed Issue 83 and my RSEM version is 1.3.1. I was following the ENCODE long rna-seq pipeline and using RSEM to calculate transcript expression from STAR transcriptomic bam.

In the log file, it says,

rsem-parse-alignments .../encode_longRnaseq/RSEM_index_hg19/RSEMref Quant.temp/Quant Quant.stat/Quant Aligned.toTranscriptome.out.bam 3 -tag XM Done!

rsem-build-read-index 32 1 0 Quant.temp/Quant_alignable_1.fq Quant.temp/Quant_alignable_2.fq Cannot open Quant.temp/Quant_alignable_1.fq! It may not exist.

I checked and the Quant.temp folder was indeed empty, but it seems rsem-parse-alignments had finished.

Could you please help me out? I can send you the bam file if it helps. Thanks!

lybird300 commented 5 years ago

Following the suggestions from here and here, I modified the STAR alignment command by (a) removing soft-clipping related parameters and (b) adding “--alignEndsType EndToEnd --alignIntronMax 1 --alignIntronMin 2 --scoreDelOpen -10000 --scoreInsOpen -10000”. The flag “--alignEndsType EndToEnd” is particularly set up to turn off soft-clipping. After that, I was able to run RSEM on STAR generated transcriptome bam files.