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alexdobin / STAR

RNA-seq aligner
MIT License
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The order of unmapped paired-end reads are not consistent #1933

Open bakerwm opened 1 year ago

bakerwm commented 1 year ago

Using the version STAR 2.5.2a to align paired-end reads to the human reference genome. Find out the order of the unmapped mates is not consistent, but the number of two unmapped files is consistent. I have no idea why some of my fastq files got the error. (Re-run the same command might go well). 

# STAR version 2.5.2a
$ STAR --genomeLoad NoSharedMemory --runMode alignReads \
    --genomeDir STAR_index \
    --readFilesCommand zcat \
    --readFilesIn demo_1.fq.gz  demo_2.fq.gz \
    --outFileNamePrefix  demo \
    --runThreadN 8 \
    --limitBAMsortRAM 10000000000 \
    --outSAMtype BAM SortedByCoordinate \
    --outFilterMismatchNoverLmax 0.07 \
    --seedSearchStartLmax 20 \
    --outReadsUnmapped Fastx \
    --outFilterMultimapNmax 20 \
    --seedPerWindowNmax 5
alexdobin commented 1 year ago

Please switch to a recent version of STAR: https://github.com/alexdobin/STAR/releases/tag/2.7.11a If it still gives an error, please send me the Log.out file.