2-pass speed about 7 M/hr
hello,
is it possible that mapping speed for the 2nd pass decreases to 7 M/hr if 900.000 new splice sites and a comprehensive gene model (gencode v19) were used for index generation.
first pass was ~100-fold faster (700 M/hr).
my concrete syntax:
/home/ws/SW_install/STAR/STAR/source/STAR --runThreadN 31 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --genomeDir $indices --readFilesCommand zcat --readFilesIn /home/ws/data/PatientData/$b/m*/$s/t*/date*/$f1 /home/ws/data/PatientData/$b/m*/$s/t*/date*/$f2 --outFileNamePrefix $name
wiht 31 cores on a 192 GByte Scientific Linux 7 workstation.
Can I do something to improve speed?
dietmar
hello,
is it possible that mapping speed for the 2nd pass decreases to 7 M/hr if 900.000 new splice sites and a comprehensive gene model (gencode v19) were used for index generation.
first pass was ~100-fold faster (700 M/hr).
my concrete syntax:
/home/ws/SW_install/STAR/STAR/source/STAR --runThreadN 31 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --genomeDir $indices --readFilesCommand zcat --readFilesIn /home/ws/data/PatientData/$b/m*/$s/t*/date*/$f1 /home/ws/data/PatientData/$b/m*/$s/t*/date*/$f2 --outFileNamePrefix $name
wiht 31 cores on a 192 GByte Scientific Linux 7 workstation.
Can I do something to improve speed?
dietmar
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