paired end data with varying read length

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5.2 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 • 1.3k views

ADD COMMENT • link updated 3.7 years ago by linyao • 0 • written 5.2 years ago by manjumoorthy95 ▴ 60

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

ADD REPLY • link 5.2 years ago by ATpoint 85k

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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 3.7 years ago by linyao • 0

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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 3.7 years ago by ATpoint 85k

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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 3.7 years ago by linyao • 0

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

ADD REPLY • link 3.7 years ago by ATpoint 85k

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