I am performing Rna-seq analysis pipeline on Arabidopsis thaliana :
I have succeeded in applying steps of indexing and mapping to the reference genome
the quantification step using Rsem tool is applied on the first two mapped files and the expected results have appeared 2 main files resulted for each mapped file 1. rsem.genes.results 2. rsem.isoforms.results
unfortunately no result files have appeared, when i tried to apply the same command on the other remaining files. Although no error have been detected for the command and only the log file has resulted from this step and contains no errors but it has data like other created log files created for the first two files
the ONLY noticeable thing is that the 2 successful mapped files are (Aligned.sortedByCoord.out.bam 263 MB) and (Aligned.sortedByCoord.out.bam 39 MB) BUT the other files have sizes (more than 900 MB)per each one I am using super computer and there is no probability of RAM failure or storage problem.
Here is the command line i use in the quantification step in general with changing the files names only:
rsem-calculate-expression --bam --no-bam-output -p 10 'data/HeatMapping/M_SRR3724798/Aligned.toTranscriptome.out.bam' 'data/RsemIndexing/ArabTair10' 'data/RsemQuantification/Q_SRR3724798/rsem' >& 'data/RsemQuantification/Q_SRR3724798/rsem.log'
Can you help me please in solving this problem?
