Closed:GRO-seq low_mapping rate

Question

[383424564]

Hi,

I get the GroSEQ Rawdata after following this protocol entitled " Global Run-On Sequencing (GRO-Seq)". First, I remove the adapter with Cutadapt and mapping with Bowtie2, results showing about 20% mapping. Then I do the other way using Trimmomatic to remove adapter, and mapping with STAR, get 40% uniquely mapping rate. My question is how to improve the mapping rate?

Thanks in advance.

Trimmomatic command:

java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar PE -phred33 KO-GRO_S0_L001_R1_001.fastq.gz KO-GRO_S0_L001_R2_001.fastq.gz output_KO-GRO_S0_L001_R1_001.paired.clean.fastq.gz output_KO-GRO_S0_L001_R1_001.unpair.clean.fastq.gz output_KO-GRO_S0_L001_R2_001.paired.clean.fastq.gz output_KO-GRO_S0_L001_R2_001.unpair.clean.fastq.gz ILLUMINACLIP:/share/apps/rc/software/Trimmomatic/0.36-Java-1.8.0_92/adapters/TruSeq2-PE.fa:2:30:10:1:true \LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50

fastqc: Some problems with "Overrepresented sequences & Per sequence GC content"

mapping

STAR --runThreadN 5 --genomeDir ref --readFilesCommand zcat \
--readFilesIn rawqcoutput/output_KO-GRO_S0_L001_R1_001.paired.clean.fastq.gz \
rawqcoutput/output_KO-GRO_S0_L001_R2_001.paired.clean.fastq.gz \
--outFileNamePrefix STARMAPPING/sample2 \
--outSAMtype BAM SortedByCoordinate \
--outBAMsortingThreadN 5 \
--quantMode TranscriptomeSAM GeneCounts

After mapping, I get few peaks view in IGV. So, I think the problem is the low mapping rate. This the first time I post my question, I don't know how to put my picture on here.

If you need more information, please does not hesitate to contact me.