Reverse read is shorter than forward read

Question

[vvs.hazia]

What might cause shorter reverse read than forward one among all samples?

Answer 1

[GenoMax]

Other than the possibility mentioned already, the reverse read may have already been trimmed for quality or some other reasons. Sometimes data from failed runs can be recovered for a certain number of cycles (so data would be accordingly short for failed read). Your sequence provider should have informed you if that was the case.

[vvs.hazia]

That was the case. Fortunately they provided as the information. Otherwise it would be really strange, cause we needed equal length of both reads. Thank you for taking part in discussion

Answer 2

[rpolicastro]

If you are referring to Illumina sequencing, the read length can be set independently for the forward and reverse read. Talk to the person(s)/core that sequenced your data for more information.

[ATpoint]

A very common scenario is single-cell sequencing with the 10X platform. Forward reads contain UMIs and cellular barcodes, reverse read the cDNA. For R1 only the first 20-something bases (depending on the exact kit) are useful while for R2 everything is useful, so one might choose to sequence as e.g. 28x91 bp as this would be in the range of a 150 cycle kit which costs half of e.g. a 300 cycle kit that would allow 2x150bp reads which, as said above, does not make sense in some applications.