Low no_Feature value after using STAR for alignment

1

![Dear BioStars community,

I used STAR 2.7.5a to do alignment for my RNA-seq data, the script is as below:

genomegenerate:

STAR --runThreadN 6 --runMode genomeGenerate --genomeSAindexNbases 9 
--genomeDir /home/xg60a/Ermin/03align_out/lsalit_STAR_genome 
--genomeFastaFiles /home/xg60a/Ermin/00ref/Lsali.fna 
--sjdbGTFfile /home/xg60a/Ermin/00ref/Lsali02.gtf 
--sjdbOverhang 149

align out:

STAR  --runThreadN 5 --limitBAMsortRAM 1101674636 --genomeDir /home/xg60a/Ermin/03align_out/lsalit_STAR_genome 
--readFilesCommand zcat --readFilesIn /home/xg60a/Ermin/02clean_data/B1_1_val_1.fq.gz, /home/xg60a/Ermin/02clean_data/B1_2_val_2.fq.gz 
--outFileNamePrefix /home/xg60a/Ermin/03align_out/B1t_ 
--outSAMtype BAM SortedByCoordinate 
--outBAMsortingThreadN 5 
--quantMode TranscriptomeSAM GeneCounts

However, after doing alignment, there are 6249540(93.12%) uniquely mapped genes but the number of no_feature genes is as many as 6438119 which even more than uniquely mapped genes. Can anybody tell me, what is the problem? Thanks a lot in advance!


RNA-seq


alignment


STAR

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