bamqc mapped reads 100%???

[qianlong kang]

input file is from STAR and sorted with samtools.

STAR command line:

STAR --runMode alignReads --runThreadN 8 --genomeDir /data2/kangql/RNA_seq_data/star_grch38/ --readFilesIn cut_scRNA_PBMC_100cell_20210603_S1_L001.fastq.gz --readFilesCommand zcat --outFileNamePrefix ./star_out/cell100/cell100 --outTmpDir star_tmp --outSAMtype BAM Unsorted --outSAMunmapped None --quantMode TranscriptomeSAM GeneCounts

bamqc command line:

qualimap bamqc -bam cell100/sorted_cell100_star.bam -outdir cell100/ -outformat PDF:HTML --java-mem-size=4G

I would be grateful if someone could help me

0.0          ^-^

[Konstantin Okonechnikov]

HI,

in the STAR command there is an option stating that unmapped reads are not provided in the BAM file (--outSAMunmapped None), therefore only mapped reads are shown in the BAM QC report.

Best regards,

  Konstantin

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[Neng Liu]

• I see! Thank you very much!^_^