paired end data with varying read length

4

Entering edit mode

4.6 years ago

manjumoorthy95 ▴ 60

I have a paired end data with forward read length of 28bp and reverse read of 120bp. Is this some sequencing error? Will this cause error while mapping the paired data to a reference Genome using tools like bwa or bowtie2?

RNA-Seq illumina insert size • 1.2k views

ADD COMMENT • link updated 3.1 years ago by linyao • 0 • written 4.6 years ago by manjumoorthy95 ▴ 60

1

Entering edit mode

Is this scRNA-seq (or any other single-cell application)?

ADD REPLY • link 4.6 years ago by ATpoint 82k

0

Entering edit mode

Hi manjumoorthy95, did you solve it. Now I have the same problem. The R1 has 74bp, but the R2 has just 9bp. And my dataset doesn't look like sing cell RNA-seq. I only have tens of samples.

ADD REPLY • link 3.1 years ago by linyao • 0

0

Entering edit mode

Well, you should know what kind of data that is. Where is it from? 9bp is indeed rather short, so either some kind of index/barcode, for sure no biological read.

ADD REPLY • link 3.1 years ago by ATpoint 82k

0

Entering edit mode

yes. 9bp is too short to have biological meaning. And I attached some information of the dataset sent from the people generating the dataset. Is it meaningful?

Type run: NextSeq protocol: R1 74bp | R2 9bp | I1 9bp PhiX spike in: 5%

ADD REPLY • link 3.1 years ago by linyao • 0

1

Entering edit mode

No clue, why don't you simply ask them. Don't guess about data, talk to people.

ADD REPLY • link 3.1 years ago by ATpoint 82k

Login before adding your answer.