Hi:
I am a bit confused about total number of reads obtained from RNA-Seq run.
In the case of a paired end run fastq should both R1 and R2 reads be counted to get total number of reads.
Example:
Sample-S was run on two lanes as 2x100 PE reads configuration.
Sample-S - R1 in lane 1 - 30Mil reads (as per FASTQ file)
Sample-S - R2 in lane 1 - 30 Mil reads
Sample-S -R1 in "lane 2" - 35Mil reads
Sample-S -R2 in "lane 2" - 35Mil reads.
If I want to know total # of reads I sequenced for Sample-S
Is it 130Mil. reads or 65Mil reads?
Question 2:
I see difference close to double between FASTQ file and reads from samtools flagstat total reads. Why is this - is this because in a paired end BAM file both R1 and R2 reads are mapped and counted.
In this case should one count both R1 and R2 reads in fastq file.
Appreciate your help.
Adrian
I am a bit confused about total number of reads obtained from RNA-Seq run.
In the case of a paired end run fastq should both R1 and R2 reads be counted to get total number of reads.
Example:
Sample-S was run on two lanes as 2x100 PE reads configuration.
Sample-S - R1 in lane 1 - 30Mil reads (as per FASTQ file)
Sample-S - R2 in lane 1 - 30 Mil reads
Sample-S -R1 in "lane 2" - 35Mil reads
Sample-S -R2 in "lane 2" - 35Mil reads.
If I want to know total # of reads I sequenced for Sample-S
Is it 130Mil. reads or 65Mil reads?
Question 2:
I see difference close to double between FASTQ file and reads from samtools flagstat total reads. Why is this - is this because in a paired end BAM file both R1 and R2 reads are mapped and counted.
In this case should one count both R1 and R2 reads in fastq file.
Appreciate your help.
Adrian
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