Run STAR for mapping , remove duplicates and read counts

[jacs]

Hi Alex,

Is it possible to run STAR for mapping, remove duplicates reads and read counts in a single command ? (I have 3' RNAseq data)

Like this:

STAR --runThreadN 16 --genomeDir STAR_GTF --readFilesIn Read1.fastq --readFilesCommand zcat --outFileNamePrefix $name --outSAMtype \
BAM SortedByCoordinate --limitBAMsortRAM 50000000000 --chimSegmentMin 20 -- --bamRemoveDuplicatesType UniqueIdentical  quantMode TranscriptomeSAM GeneCounts --outReadsUnmapped Fastx --outWigType bedGraph --outWigNorm RPM

Thanks,

regards,

jacs

[Alexander Dobin]

Hi @jacs,

no, the bamRemoveDuplicates has to be run after the mapping and sorting of the BAM is completed.

Cheers

Alex