very low mapping rate of polysome profling seq
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3.0 years ago
17318598206 ▴ 20

when i use sequencing data from SRR7695423

frist, i use fastp to trim raw reads: fastp -i r1_fastq.gz -I r2_fastq.gz -o r1_trimmed_fastq.gz -O r2_trimmed_fastq.gz

then i use STAR to align: STAR --runThreadN 20 --genomeDir index --readFilesIn r1_trimmed_fastq.gz r2_trimmed_fastq.gz --readFilesCommand 'zcat' --outFileNamePrefix sample_ --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts

my mapping rate is ~20%, this is why?

RNA-seq mapping low rate • 502 views
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