STAR RNA-seq aligner yields different read length than fastqc/zcat?

[LeonDK]

Hi all,

I've noticed that the STAR RNA-seq aligner yields different read length than fastqc/zcat? Maybe there is something I have misunderstood?

star --version
STAR_2.4.0i

fastqc --version
FastQC v0.11.2

Then under the ’Sequence Length Distribution’ section, it says that the read length is 101bp. I can confirm this using zcat and gawk:
zcat mySample.fastq.gz | head -n2 | tail -n1 | gawk '{print(length($0))}'
101

HOWEVER the STAR output file ‘Log.final.out’ disagrees:
cat mySample/Log.final.out | grep 'Average input read length'
Average input read length | 200

Comments?

Cheers,
Leon

[alexdobin]

Hi all,

I've noticed that the STAR RNA-seq aligner yields different read length than fastqc/zcat? Maybe there is something I have misunderstood?

star --version
STAR_2.4.0i

fastqc --version
FastQC v0.11.2

Then under the ’Sequence Length Distribution’ section, it says that the read length is 101bp. I can confirm this using zcat and gawk:
zcat mySample.fastq.gz | head -n2 | tail -n1 | gawk '{print(length($0))}'
101

HOWEVER the STAR output file ‘Log.final.out’ disagrees:
cat mySample/Log.final.out | grep 'Average input read length'
Average input read length | 200

Comments?

Cheers,
Leon

Hi Leon,

STAR outputs the total length of the paired-end read. If you have 2x101b reads, and you trimmed adapters, average length of 200b would make sense.

Cheers
Alex

[LeonDK]

Hi Leon,

STAR outputs the total length of the paired-end read. If you have 2x101b reads, and you trimmed adapters, average length of 200b would make sense.

Cheers
Alex

Hi Alex,

Thanks for input (again)

Makes sense! Might I suggest incorporating a small note reg. this? E.g.:
'Average read length of both PE reads'

Cheers,
Leon