How To Extract And Quantify Duplicated Rna-Seq Reads?
I am working on a RNA-Seq data. The Fastqc shows that data has duplication level of >65%. Can anyone tell me how I can extract the duplicated reads and quantify them? I am also interested to rank those duplicated reads.
Thanks!
• 4,916 views
•
link
updated
by
Zev.Kronenberg
•
written
by
Pals
•
written
by
Pals
1 answer
After marking duplicates (with your favorite program) you can use the samtools flag to pull out the reads you want.
Just set the include flag: samtools view -f 0x400:
0x400 PCR or optical duplicate
• 254 views
•
link
written
by
Zev.Kronenberg
Log in to answer this question.
More posts like this
-
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
written by eager_underdog •
-
fastp json -> multiqc and fastp processed reads ->fastqc -> multiqc show different level of sequenc…
written by Rakesh Tiwari •
-
Is it possible to extract miRNAs from RNA seq data?
written by abdul.suboor123 •
-
"Normal" percent duplication for RRBS reads?
written by eb13 •
-
GC content for RNA-Seq data
written by sukesh1411 •
-
Adapter trimming - Nextera XT dual indexes
written by Pinki •
-
Mate Pair Read Duplication Level
written by abc •
-
Illumina Mate Pair Read Duplication Level
written by abc •
-
Error While Running Trinity Rna-Seq Assembler
written by pjyoti29 •
-
Domain-Based Clustering Of Protein Structures
written by Pals
Why do you want to extract and quantify them? They are already quantified by FastQC right? Are you worried about the big number? Then you should Duplicated Reads In Rna-Seq Experiment where it is explained that in RNA-seq many of the reads come from ribosomal RNA and highly expressed genes resulting in a high duplication level in your reads
just curious to see the actual reads that are duplicated thousands of times.
gunzip -dc yourFastq.gz | awk '{if(NR%4==2)print $0}' | sort | uniq -c
Thank you very much Irsan. I had to slightly modify your trick awk '{if((NR-2)%4==0)print $0}' :-)
Cool, I changed the comment
Unfortunately, sorting did not go well. I want the most repetitive sequence ranked, where this command sorts alphabetically.
print the reads and then | sort | uniq -c
Thank again, finally its done. gunzip -dc yourFastq.gz | awk '{if(NR%4==2)print $1}' | sort | uniq -c | sort -g
glad you go it working.