gravatar for anamaria

5 hours ago by

Hello,

I am doing RNA-seq analysis.
I will have these steps performed:

hisat2 -p 12 --new-summary --summary-file $OUTPUT.hisat2.summary -x $REF -1 $R1  -2 $R2 -S $OUTPUT.sam

#1-Convert sam to bam
 samtools view -bS -o $OUTPUT.bam $OUTPUT.sam

# 2- Sort bam file
 samtools sort $OUTPUT.bam  -o $OUTPUT.sorted.bam

# 3- Generate index for bam file
 samtools index $OUTPUT.sorted.bam

I know that I get number of mapped and unmapped reads with:

samtools view  -b -f 2 $OUTPUT.bam > mapped.bam
samtools view  -b -F 2 $OUTPUT.bam > unmapped.bam

Can someone please recommend me a code to make a plot like attached?

enter image description here

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modified 4 hours ago

written
5 hours ago
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anamaria140



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